Not having a specific case before us, I can't nail down exactly what I would propose. However, I was more thinking along the lines of using the writers guide as some of the evidence that might help resolve the issue between two pieces of mutually inconsistent canon.
I tend to agree on this point, a good example, I think, might be Kirk's cabin? On screen it's repeatedly stated that it's on deck five, except one time when it's on deck fourteen. In the face of this (gasp) can
n contradiction, we can refer to TMoST where it is established that it is indeed supposed to be on deck five. Therefore we can reasonably conclude that the deck fourteen reference is, exactly what it was, a mistake. Of course, ones mileage will inevitably vary.