There are a few red flags that show up again and again in certification projects: weak document control, inconsistent inspection evidence, missing internal audits, poor management review discipline, and corrective actions that never truly close.
Another major red flag is relying on generic templates that do not match the actual operation. When the documented system and the real process are disconnected, the audit gets harder and employee confidence drops.
The best way to avoid these issues is to start with a realistic assessment and then build the system around real workflows.