Manufacturing Deficiencies: Common FDA Quality Issues in Pharma and Medical Devices

The FDA doesn’t just check labels or packaging. It digs into the manufacturing process-the real heart of drug and device safety. In 2025, warning letters from the FDA revealed a troubling pattern: the same basic failures keep showing up, again and again, putting patients at risk. These aren’t random mistakes. They’re systemic breakdowns in how companies manage quality. And the FDA is responding with more inspections, tougher penalties, and a new focus on culture, not just paperwork.

Aseptic Processing Failures: The Silent Killer

One in every two warning letters in 2025 cited problems with aseptic processing. That’s the method used to make injectable drugs, IV solutions, and sterile medical devices without letting bacteria or viruses in. If this step fails, the product can kill people.

The FDA found facilities where workers didn’t properly validate their sterile environments. Media fill studies-simulations that test whether contamination can creep in during production-were either missing or flawed. In one case, a company used a glove box that wasn’t sealed correctly. In another, staff skipped gowning procedures because they were rushed. These aren’t minor oversights. They’re direct paths to deadly infections.

The FDA expects companies to prove sterility isn’t just luck. It requires repeated testing, environmental monitoring, and training that’s documented and followed. When these controls are ignored, the FDA doesn’t just issue a warning. It blocks the product from entering the U.S. market.

Data Integrity: When the Records Don’t Match Reality

Thirty-nine percent of 2025 warning letters targeted data integrity failures. This means the records didn’t reflect what actually happened on the factory floor. Some companies used erasable pens to correct batch records. Others deleted electronic logs or turned off audit trails on testing instruments like UV-Vis spectrometers.

The FDA’s ALCOA+ standard isn’t optional. Data must be:

• Attributable
• Legible
• Contemporaneous
• Original
• Accurate
• Plus complete, consistent, enduring, and available

One Chinese manufacturer was caught using laminated sheets with pencil notes-easily changed, never traceable. Another deleted raw data after passing a test, claiming it was "redundant." The FDA doesn’t accept that. Every test result, every adjustment, every correction must be recorded and preserved for at least 180 days. Electronic systems must lock users out if they try to delete data. No exceptions.

Material Control: Dangerous Ingredients Slip Through

Bad raw materials can turn a safe product into a poison. In 2025, the FDA found multiple cases where suppliers weren’t properly vetted, and incoming materials weren’t tested for deadly contaminants.

One company used glycerin in its toothpaste that hadn’t been checked for diethylene glycol (DEG)-a toxic chemical linked to kidney failure. Another didn’t verify whether its sorbitol supplier was testing for ethylene glycol (EG). Both are common industrial solvents that can accidentally contaminate pharmaceutical ingredients if the supply chain isn’t tightly controlled.

The FDA requires manufacturers to test high-risk materials using validated methods. For DEG and EG, that means testing down to 0.1% concentration, as outlined in USP <1085>. Supplier audits aren’t optional. You can’t just trust a certificate of analysis. You have to prove the supplier’s testing is reliable. That means on-site visits, sample retesting, and documented agreements.

Process Validation: Making Things Work-Consistently

Just because a product works once doesn’t mean it will work every time. That’s why process validation is required. In 2025, 28% of warning letters cited missing or incomplete validation studies.

One company made toothpaste in large batches but never tested whether the mixing process evenly distributed active ingredients. Another used a new tablet press but didn’t prove it could consistently hit the right hardness and dissolution rate. The FDA expects three consecutive successful batches under normal production conditions, with every step monitored and recorded.

Validation isn’t a one-time task. It’s an ongoing commitment. If you change a machine, a supplier, or a formula, you must revalidate. Skipping this step means your product’s quality is guesswork-and the FDA treats guesswork as a violation.

Quality Culture: The Root Cause Behind Every Failure

Behind every data entry error, every skipped test, every unvalidated process is a deeper problem: culture. According to experts analyzing 2025 warning letters, 78% of facilities showed leadership that prioritized speed over compliance.

Managers pushed teams to meet deadlines even when controls weren’t ready. Quality teams were underfunded and had no authority to stop production. Employees were afraid to speak up. One company admitted in its response letter: "This site does not prepare batch production records for every batch of our listed drug." That’s not incompetence. That’s indifference.

The FDA’s new Quality Management Maturity (QMM) program, launched in early 2024, is designed to catch this. It doesn’t just check boxes. It asks: Does leadership own quality? Are employees trained to stop the line? Is quality measured in metrics, not just audits?

Companies that fix their culture see 63% fewer repeat violations. The FDA is now using QMM results to decide who gets inspected more often-and who gets a break.

Where Are These Problems Happening?

While violations occur globally, patterns are clear. In 2025:

• Chinese facilities were cited 28 times for poor analytical method validation
• Indian facilities saw 24 warnings for data integrity failures
• Malaysian sites were flagged 9 times for weak quality unit authority

The FDA increased unannounced inspections by 40% in 2025, and 68% of those targeted facilities in Asia. Many of these companies had never been inspected before. Now, they’re on Import Alert 66-40-meaning their products are blocked from entering the U.S. until they prove they’ve fixed the issues.

Even domestic U.S. facilities aren’t safe anymore. The FDA plans to conduct 1,200 unannounced inspections in 2026-up from 850 in 2025. No one is exempt.

What Happens When You Get a Warning Letter?

Getting a warning letter isn’t the end-but it’s the start of a long, expensive road. In 92% of 2025 cases, the FDA required companies to hire an independent CGMP consultant. The average remediation time? 6 to 18 months.

Fixing data integrity? You need validated audit trails, user access controls, and 180-day record retention. Fixing aseptic issues? You need full media fill studies, environmental monitoring, and staff retraining. Fixing material controls? You need supplier audits and validated testing protocols.

And it’s not just about fixing the problem. You have to prove it won’t happen again. That means new training programs, updated SOPs, and internal audits that actually find issues before the FDA does.

What’s Next for Manufacturers?

The FDA’s focus is shifting. It’s no longer just about checking if you followed the rules. It’s about whether you have a culture that makes compliance automatic.

Emerging areas of scrutiny include:

• Cloud-based quality systems-12 warning letters in 2025 cited poor controls
• Contract labs-8 letters found insufficient oversight of outsourced testing
• Continuous manufacturing-5 letters questioned validation of new tech

Spending on compliance solutions hit $4.7 billion in Q3 2025. That’s up 12.3% from last year. Companies are realizing: paying for quality now is cheaper than getting shut down later.

The message is clear: if your manufacturing process isn’t built on science, transparency, and accountability, you’re not just at risk of a warning letter. You’re risking lives-and your business.