Most Prevalent GMP Manufacturing Issues of the Past Year

September 9, 2026

Guest article provided by BioBoston Consulting for InstantGMP

There is no single regulatory database that provides a definitive ranking of GMP failures across the entire pharmaceutical and biotechnology industry. However, recent FDA warning letters and enforcement actions provide a useful picture of the problems that continue to appear across regulated manufacturing operations.

Several themes stand out: data integrity, inadequate investigations, ineffective CAPA, quality-unit oversight, process control, and weaknesses in computerized systems. These issues are not necessarily new. What is important is that they continue to surface despite years of regulatory guidance and increasing investment in quality systems and digital technology.

For manufacturers, the message is less about reacting to individual observations and more about understanding what these recurring findings reveal about the state of the overall quality system.

1. Data Integrity Continues to Be a Major Concern

Data integrity remains one of the most important areas of GMP compliance.

Regulated manufacturers need to demonstrate that records are attributable, accurate, complete, reliable, and maintained throughout their lifecycle.

Problems can arise from surprisingly ordinary practices.

Shared user accounts
Uncontrolled spreadsheets
Inadequate audit-trail review
Missing original records
Inappropriate changes to electronic data
Incomplete documentation

Each may appear to be a relatively small issue, but together they can undermine confidence in the organization’s records.

Recent FDA enforcement continues to demonstrate this concern. For manufacturers, the practical lesson is clear: compliance depends not only on generating data, but on being able to demonstrate that the data can be trusted.

2. Inadequate Investigations Remain a Recurring Weakness

Manufacturing deviations are inevitable in complex operations. Poor investigations should not be.

A strong investigation should establish what happened, determine the potential scope and impact, evaluate relevant data, identify root and contributing causes, and determine appropriate corrective action. Recent regulatory findings continue to show what happens when this process is incomplete.

FDA’s 2025 warning letter to Catalent Indiana included concerns around inadequate investigations, including insufficient supporting information and inadequate assessment of potentially affected products and CAPA effectiveness.

The broader lesson is that an investigation should not be treated as an administrative exercise whose primary purpose is to close a deviation. It is a quality decision-making process.

3. CAPA Effectiveness Is Just as Important as CAPA Completion

Many organizations have formal CAPA processes. The challenge is ensuring that those processes actually prevent recurrence. A CAPA can be assigned, implemented, documented, reviewed, and closed while the original problem remains capable of happening again. This is why effectiveness checks matter. Manufacturers need to establish whether corrective actions changed the conditions that caused the original problem.

For quality leaders, this means CAPA metrics should go beyond the number of actions closed on time.

Useful measures can include recurrence rates, overdue effectiveness checks, repeat deviations, and the number of CAPAs that require escalation or additional action.

4. Quality-Unit Oversight Remains Fundamental

GMP compliance ultimately depends on effective quality oversight. Quality units need sufficient authority, independence, information, and resources to perform their responsibilities effectively. That includes oversight of investigations, batch documentation, laboratory data, change control, CAPA, procedures, and manufacturing operations.

Recent FDA enforcement has continued to highlight deficiencies involving quality-unit oversight, GMP records, document control, and data integrity. The issue is not merely administrative. If the quality unit cannot reliably determine what happened during manufacturing, it becomes much harder to make defensible decisions about product quality and release.

5. Digital Systems Are Creating Both Opportunities and New Risks

The shift from paper to electronic systems can improve traceability and reduce manual errors.

But electronic systems also introduce their own compliance considerations. Access controls, audit trails, electronic signatures, system changes, validation, user permissions, data retention, and system governance all need appropriate controls. This is particularly relevant as manufacturers adopt electronic batch records and integrated manufacturing platforms.

For example, InstantGMP’s manufacturing and quality platform integrates electronic batch records with inventory and quality management. Its platform is designed to bring manufacturing, quality, and related records into connected workflows rather than leaving critical information across separate manual processes.

For organizations moving away from paper records, this type of integration can provide greater visibility into how materials, manufacturing activities, quality events, and documentation connect. But digitalization still needs to be supported by appropriate validation and quality governance.

6. Manufacturing Process Control Cannot Be Overlooked

The growth of digital quality systems does not change one fundamental GMP expectation: manufacturing processes must remain under control. Recurring process deviations, contamination events, unexplained variability, equipment failures, and significant investigation backlogs can all indicate that a manufacturing process needs deeper assessment.

Recent FDA enforcement has highlighted concerns involving contamination, deviations from validated manufacturing processes, and backlogs in deviation investigations.

For manufacturers, isolated events should therefore be evaluated in context.

A single deviation may be an isolated incident.

A pattern of similar deviations may be evidence of a systemic process-control problem.

What Should Manufacturers Do About These Recurring Issues?

The answer is not necessarily to add another procedure.

In many cases, organizations need to strengthen the connection between their processes, people, technology, and quality oversight.

A practical approach includes several elements.

Look for trends rather than isolated events. Recurring minor deviations can reveal a larger systemic issue.
Strengthen root-cause investigations. Investigations should be evidence-based and appropriately scoped.
Measure whether CAPAs actually work. Closure alone is not proof of effectiveness.
Review electronic-system controls. Access, audit trails, signatures, validation, and change control should receive appropriate attention.
Connect manufacturing and quality information. When information is distributed across multiple systems, establishing the complete history of an event can become unnecessarily difficult.
Test inspection readiness before an inspection occurs. Organizations should be able to retrieve records, explain decisions, demonstrate controls, and show evidence of effectiveness without relying on last-minute preparation.

The Role of Integrated GMP Technology

Technology is increasingly becoming part of the solution to these challenges.

An integrated manufacturing platform can connect activities that traditionally existed in separate systems. InstantGMP provides electronic batch records, inventory management, quality management, and document management within its broader manufacturing environment. Its electronic batch record functionality includes version control, traceability, electronic signatures, and audit trails.

The objective is not to eliminate the human element from GMP.

Rather, well-designed digital workflows can make it easier for people to follow the appropriate process and create reliable evidence of what occurred.

Combining Technology with Quality Expertise

GMP compliance sits at the intersection of technology, process, people, and regulatory expectations. A manufacturer may have a sophisticated digital platform but still have weak investigations. Another organization may have experienced quality professionals but struggle because critical information remains trapped in disconnected paper records and spreadsheets. The strongest approach considers both sides.

BioBoston Consulting supports life sciences organizations with GMP compliance, QMS, validation, data integrity, regulatory strategy, and FDA inspection readiness.

That perspective becomes increasingly valuable as manufacturers modernize their quality infrastructure, implement electronic systems, or prepare for regulatory scrutiny.

The Bigger Lesson From the Past Year

Recent GMP findings do not point to one single failure within pharmaceutical manufacturing.

Instead, they reveal a recurring pattern.

Problems become more difficult when data cannot be trusted, investigations do not reach the real root cause, CAPAs do not prevent recurrence, quality units lack sufficient oversight, computerized systems are poorly controlled, or manufacturing processes drift away from their validated state.

The most resilient manufacturers are therefore moving toward a more integrated approach. They are connecting manufacturing and quality data, strengthening investigation and CAPA processes, improving electronic controls, and testing their readiness before regulators arrive.

Ultimately, GMP compliance is not about creating more paperwork.

It is about being able to demonstrate, with reliable evidence, that the organization understands its processes, controls its risks, and consistently produces quality products. That is the standard manufacturers should be working toward, not simply passing the next inspection, but building an operation that remains in control every day.