Hello there, there is no general rule for what is considered an acceptable compliance, however, for EU the 95% provided in the MHRA inspectors' presentation still seem reasonable. If you have a pronounced dip in compliance, it might be good to notify the authorities pro-actively to indicate that you are aware of the problem and you're addressing it. In this case, you should also include a description of your corrective/preventive action. MHRA used to do their own compliance checks and they would write to the QPPV if compliance for the last quarter was below 90%, requesting an explanation. I believe with the new EV functionality, the EMA compliance checks will be resumed (they did a pilot some years ago) and they may carry on the MHRA's practice. It might be worth checking EMA's procedures (I believe they are all published on the website) to see whether they have any provisions for this.
In US, tolerance for late submission is much lower and US PV functions usually aim for a compliance of at least 98%.