I want to tell physicists: if we are interested in knowledge, wouldn't it be more productive to fully display our confusion and our disagreements?
C. Rovelli in a discussion at the “Conceptual Foundations of Quantum Field Theory” Conference
In order to progress, we must recognize our ignorance and leave room for doubt.R. Feynman
If we worked on the assumption that what is accepted as true really is true, then there would be little hope for advance.
Professors want to avoid that their students get confused. The time they spent reading and thinking about the things that confuse them, is time they do not spent on calculations. You can't make a career in physics by being confused all the time. You need to produce papers. Hence professors “protect” their students by not discussing deep issues and things they don't understand fully themselves. They tell the standard stories and then demand that students start calculating. That's the only way how their students can be successful in the current physics system.
However, to achieve real progress we need to understand what we don't understand. Acting like everything is well understood is extremely damaging. In the words of Feynman:
Science is the belief in the ignorance of experts
Almost nothing in physics is understood completely. Physics has no fundamental axioms. In addition, even the things that seem certain, like theorems, can turn out to be wrong. While the proof may be correct, the assumptions can always turn out to be completely wrong. Nature likes to surprise us and doesn't care about what we find reasonable.
You'll only notice such things if you leave the well-paved road and start exploring narrower paths. While a lot of work, looking behind the curtain is extremely rewarding.
How wonderful that we have met with a paradox. Now we have some hope of making progress. Niels Bohr
Here are two examples: