In my opinion it sounds like you are approaching this the wrong way. I would start by addressing the issues to eliminate them on the front end (in the field) rather than doing damage control on the back-end (processing). Think "junk in = junk out"
Create a checklist that includes each of the camera settings and make sure you verify them before flying. We reference a checklist before every takeoff to make sure everything (camera settings, drone settings, etc.) is where it needs to be before you fly.
The same goes for the GCP's. Communicate with whomever is placing the GCP's for you and explain to them that they are necessary to deliver quality data. If they are not placed how you have specified before the mission then you cannot guarantee the results. That should be a pretty easy one to address I would imagine. As a last line of defense, since you know where the GCP's are supposed to be, I suppose you could do a manual flight to each GCP location before you start mapping so that you can verify its presence.