One problem I have come across is that many instructors fly C172's and PA28's. The C172 uses 10 deg of flap and the (most if not all) PA28 25 deg for s/f. Most instructors can't be bothered to read the POH and hence don't know this. I just about had a row with a FI early on in my flying when doing a s/f take off in a PA28 from a grass airfield...he insisted I use 10 deg, I said that we should use 2 stages, and of course after a discussion at the end of the runway he "won" being the more experienced.....and we survived.
I've also known instructors crash headlong into a mountain and kill themselves, so the moral of that story is that don't just accept what they say if you have any doubt, no matter how experienced they think they are (this goes for anyone, not just FI's of course).
PS I was right, I read the POH later.