What does obedience entail when one is at seminary?

Is there any recourse for students who may not agree with what some of their professors are trying to teach them?

Show up for what you're supposed to show up for. Don't be disruptive. If you don't agree with a teacher ... don't argue. Sometimes there's room in the class for discussion, sometimes there isn't. If there isn't, let it go. If there is, don't overdo it.

Would you say the same holds for religious in in-house formation, Theo or Phil?

I have no experience of that, but I should think so. The big difference would be that if the error were pervasive, I might wonder if this particular order was truly the right one for me.