Root Causes of Late or Inaccurate Shipments

By Bekah Tatem, Sr. Content Writer

Last Updated April 8, 2026

8 min read

In this article, learn about:

Common internal, external, and unpredictable causes of late or inaccurate shipments

How to diagnose which root causes are behind your specific shipping issues

Practical steps to reduce shipment problems and avoid costly chargebacks

The impact of shipping issues is rarely isolated to a single part of your business. Shipping issues have ripple effects, impacting your relationship with retailers, the satisfaction of your customers, your brand reputation, and your bottom line.

Ongoing and recurring shipment issues can lead to major consequences and financial implications. The frustrating piece is that many times, it can be difficult to pinpoint the source of the shipping issues, and sometimes the issues are outside your control.

In this article, we’ll dive into common root causes of late or inaccurate shipments, grouped into three categories:

Internal root causes: areas you can directly control

External root causes: areas you can influence but not fully own

Unpredictable root causes: Circumstances you can’t prevent but can plan and build resilience for

Internal Root Causes

Internal root causes originate from within your business. They often stem from issues with processes, systems, and data. While being responsible for shipping issues may be stressful, the silver lining is that these issues can be directly addressed through clearer processes.

Let’s take a look at common root causes of internal issues:

Inventory Management Issues

If you don’t have the right product in the right place at the right time, even the best warehousing and shipping practices can’t save the shipment.

Common Issues	Root Causes	Ways to Improve
Chronic stockouts or last-minute production that lead to missed ship dates	Inaccurate forecasts that don’t reflect true demand patterns.	Use historical sales plus retailer point of sale data to refine forecasts. Hold regular demand review meetings. Track performance by customer and channel to improve forecast accuracy.
Inventory inaccuracies between systems and physical stock	Poor inventory controls and processes; lack of standardization for how product moves through your warehouses; non-standardized or manual documentation processes.	Standardized stock handling processes. Implement systems that allow for real-time inventory updates. Use barcode scanning or RFID when possible. Conduct regular cycle counts to reconcile differences before they get out of hand.
Phantom inventory (system shows stock that doesn’t exist)	Infrequent or ineffective cycle counts; data entry errors; failure to make adjustments for damage, shrink, and mis-picks.	Run regular phantom inventory analysis by comparing recent sales, inventory data, and past trends to spot stores where sales suddenly stop even though inventory shows available stock.

Order Management Problems

Errors at the order level ripple all the way down the fulfillment chain. If the order is wrong, the shipment will be wrong, regardless of if it was on time.

Common Issues	Root Causes	Ways to Improve
Incorrect item numbers, quantities, or ship-to locations	Manual data entry with validation; outdated or inaccurate item master data.	Standardize or automate order-entry workflows with required fields and approvals. Ensure master item data is accurate, including the correct inner/outer pack sizes, units per case, and ordering quantities.
Missed retailer order changes, cancellations, or expedites	Having no defined owner for handling order changes; poor documentation of how and when to apply order changes; timing issues, like shipping orders before the window for changes has closed.	Define a single team or role that owns order changes. Handle all changes through one standardized process. Use integrated systems, like an ERP, that will reflect order changes across your business. Set clear standards around order change windows and communicate them with retailers.
Manual re-keying of orders between systems (e.g., manually moving data from retailer portal to ERP or WMS)	Lack of EDI or legacy systems that aren’t integrated; reliance on manual order processes, like spreadsheets, emails, etc.	Automate orders from retailers using EDI or APIs. Utilize ERP or WMS to provide retail-time visibility into inventory and orders.

Related Reading: B2B Integrations: EDI and API

Documentation Inaccuracies

Even when the product and timing are right, incorrect documentation can lead to delays, refusals, or chargebacks.

Common Issues	Root Causes	Ways to Improve
Mismatches between your physical shipment and the Advance Shipment Notice (ASN)	ASNs created before picking and packing is finalized; manual keying of quantities or cartons; last-minute order changes that aren’t reflected in the ASN.	Integrate WMS/ERP with your EDI system so ASNs are generated from pick and pack data. Add validation to compare ASN data against shipment data. Review and track ASN-related chargebacks to identify recurring patterns or problem areas.
Missing or incorrect PO number on documentation (ASNs, labels, invoices)	Incomplete or incorrect order data; manual document creation; not double-checking documents for accuracy.	Make PO number a required field in order entry and document creation. Have a single source of truth for PO numbers, instead of re-keying. Add automated checks that block documents from being sent or printed without a valid PO.
EDI errors	Outdated or incorrect EDI maps; missing or invalid data; manual interventions or “workarounds” that bypass controls.	Regularly review and update EDI maps if retailers change requirements. Use a trusted provider to automate EDI for your business. Monitor EDI error logs to promptly address issues.

Compliance Failures

Retailers expect you to follow their routing guides and requirements precisely, outlining procedures for:

Packing materials
How items are packed and stacked (carton and pallet configuration)
Shipment windows and delivery appointments
On-time, in-full (OTIF) performance
Labeling requirements (carton, pallet, SSCC/UCC‑128)
Required documents (ASNs, packing lists, invoices, BOLs)

Non-compliance frequently leads to fines and chargebacks and can quickly become a drain on your profits. The tricky part is that each retailer has their own set of expectations and standards. To stay ahead, your business needs a systematic way to understand, track, and operationalize retailer’s rules across your teams and systems. For an in-depth look at staying compliant with retailers, check out the Vendor Compliance Checklist.

External Root Causes

External root causes occur outside your four walls, oftentimes stemming from carriers, 3PLs, retailers, or other partners. You may not control these factors directly, but oftentimes you’re still accountable for the result.

However, a mindset of “we can’t control that” can quickly turn into a loss center if long-term issues go unaddressed. The key is to move to a mindset of risk management and influence.

While you may not have direct control over external issues, you still have the power to choose better partners, set expectations clearly, and design processes that minimize the impact when external issues do arise.

Some areas where external issues can pop up include:

Third-party provider issues:
- Carriers or 3PLs missing pick-ups or delivery appointments
- Poor communication on delays, exceptions, or damages
- Lack of visibility to support problem-solving, like missing carrier tracking updates or proof of delivery

Retailer errors:
- Retailers sending incorrect or incomplete POs (wrong items, dates, or shipping info)
- Last-minute order changes or cancellations that aren’t clearly communicated
- Incorrect receiving, scanning, or check-in processes at the DC or store

Logistics issues:
- Traffic, port congestion, or labor disruptions
- Regulatory or customs delays for cross-border shipments
- Infrastructure challenges, such as limited dock capacity at either end

Best practices for improving processes and minimizing impact:

Strengthen your partner selection and hold partners accountable: Define clear service-level expectations and regularly review carrier/3PLs performance to identify chronic underperformers.
Create clear communication and escalation paths: Establish processes around who notifies whom when delays, misses, or damages occur. It’s also important to ensure customer service, sales, and retailer contacts are looped in early, not after the fact.
Build flexibility and buffers into your logistics plan: Use realistic lead times and, where possible, ship earlier within the window to anticipate disruptions.
Align closely with retailers on expectations and exceptions: Confirm routing guides, ship windows, and appointment requirements regularly.
Leverage data and visibility tools: Use transportation visibility (track-and-trace) to spot at-risk shipments early.

Related Reading: How to Select a Freight Carrier

Unpredictable Root Causes

Not every shipment issue can be traced back to a misstep or broken process. Some disruptions are truly unpredictable. Natural disasters, economic disruptions, and technology failures are just a few examples of where things can go wrong.

These events are not preventable, but you can prepare your team for how you will respond when they happen. Building a resilient and flexible supply chain is your best defense against these types of disruptions.

Below are three common categories of unpredictable root causes and how you can prepare.

Weather, Natural Disasters, and Infrastructure Disruptions

Severe weather and natural disasters can bring even the best-run supply chains to a halt. Major storms, floods, fires, or hurricanes can close facilities, shut down ports, or make key transportation routes unusable for days or weeks.

Ways to prepare:

Build contingency routing options and backup carriers
Develop emergency communication plans for notifying retailers of delays
Identify critical SKUs and customers that get priority in a disruption

Sudden Market or Economic Shocks

There’s a variety of external market and economic forces that can disrupt your supply chain, including:

Sudden spikes in demand due to viral trends
Labor strikes or abrupt workforce shortages
Unexpected regulatory changes, like tariffs, affecting shipping or product movement
Economic or global shocks, such as recessions, geopolitical conflicts, or pandemics

The COVID‑19 pandemic is a prime example of unpredictable disruption. It combined demand spikes, labor disruptions, transportation constraints, and new regulatory and safety requirements all at the same time.

Ways to prepare:

Maintain some flexible capacity (labor, production, or 3PL support).
Use scenario planning for peak or surge conditions.
Establish escalation paths and decision-makers for crisis situations.

Technology and System Outages

Technology failures and outages can grind shipping operations to a halt. In addition, cybersecurity incidents can lock users out of critical systems or compromise data, slowing operations while issues are investigated.

For example, in July of 2024, an outage of CrowdStrike software crashed Windows systems worldwide. The outage grounded thousands of flights, briefly shut down or slowed operations at major ports and railroads, and created days or even weeks of disruption.

How to prepare:

Define manual backup processes for critical shipping functions (e.g., paper pick tickets, offline label templates, manual BOLs).
Regularly test business continuity plans so teams know how to operate when systems are down.
Work with IT and key partners to reduce single points of failure and clarify recovery time objectives for core systems.

Related Reading: What is Supply Chain Resilience?

Recover Lost Revenue with SPS Commerce

When things don’t go as planned, you can expect retailer deductions to start flowing in. But managing retailer deductions doesn’t have to be complex. SPS Commerce offers cutting-edge software to help suppliers dispute deductions, maximize cash flow, and uncover critical data insights.

See how SPS Revenue Recovery can save you time and help you recover your hard-earned money!