I think the terminology and rule here is less important than the logic. In my opinion logic is a much more reliable way to determine if a sentence is well written or not.
First, I'm not sure which word your teacher thinks "which" modifies; seems to me it modifies the whole phrase. Notice how I just used which ... it modifies "word" which comes after, not before ... so I think perhaps your teacher feels there's a flaw, but didn't explain it well. While your sentence appears grammatically correct, when you consider the intended meaning there's room for improvement. When you put a phrase between commas it means you could remove it without changing the meaning of the sentence. If you remove "which forces the learner to concentrate" the sentence still makes grammatical sense. However, you have removed a piece of information that is necessary to the reader's understanding. Therefore, I suggest "It seems moving the body while learning forces the learner to concentrate, enhancing memory [retention]." Notice I removed "that;" it's unnecessary. I'm also wondering about the word "seems." Is this something that you've provided proof of or not? I would expect so. If so, the "seems" makes your statement wishy-washy. If you haven't provided evidence for this theory ... well ... you probably should.