If something did seem to be pulled out of thin air, I asked critical questions, did my own research, or just made a mental note that it's note quite as much a fact as it's made out to be. I can't think of any examples off-hand, but probably it was with stuff in sociology, where (I feel) there are so many variables it's nearly impossible to attribute an outcome to a specific type of behavior.
I think it's up to each person to think critically, and I think each person has the power to control whether or not they "switch off" their brain. It just so happens most people choose not to.
The concern you have about most educational environments is why I'm an "unschooling"-leaning eclectic homeschooler for my own children. There are at least biological drives ensuring that my children will disagree with me [smile], so they all learn to question one teacher.
If it was limited to subjects where students could study the evidence and come to their own conclusions, school would quickly end up being useless...
In lower level courses, where straight up lectures are more common, professors are more inclined to simply teach the facts instead of trying to create a(n unmanageable) discussion between 50+ people. Which is understandable. And they (usually, at the beginning of the semester, at least) stress that they have office hours or are available at other times if someone wants to continue talking about a topic for whatever reason.
But these are my experiences, maybe I've just been lucky?
If you're in a class and you don't think what the professor is saying is right, either ask a question or write a note so you can follow up on it later.
Not once in my undergraduate career was I expected to turn off my brain and go on cruise control just because the guy down in front was an expert.
Honesstly, I feel like my whole benefit of my academic career was taken from sitting in a class, not understanding what the fuck was going on and then struggling to understand or contradict what I was being taught.
Critical thinking has become a second-class citizen in our educational system.
Even if what you've "learned" is correct, you've disengaged yourself from the actual process of thinking and learning.