"Clarifies" was the wrong choice of word.
The first sentence says that all students take both classes. The second says that some students take both classes. If all students take both classes, then it is also true that some students take both classes. Therefore, the second sentence does not contradict the first sentence, but is contained in it AS IT IS CURRENTLY WORDED.
HOWEVER, if the problem had been worded correctly, " ... students take calculus OR physics" THEN the second sentence WOULD HAVE clarified that the OR was intended to be an inclusive OR (just in case the student had any doubt).
I agree with your point, though. All real learning takes place inside a student's head. When students understand something, they have an obligation to themselves to speak up, to have it explained to them. If they do not like the explanation, they should be able to say, "I have no choice but to acquiesce to your answer, but I don't agree with it."
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