There is a bit of a mismatch. The question asks who [whom] you have worked with. It asks, a priori, about (a) people you worked with but no longer work with and (b) people you have been working with, i.e., people you are still working with.
A reply that answers about people in either class, (a) or (b), is appropriate, as is a reply that answers about people in both classes.
So the student's answer is OK in being limited to class (b). But it's possible that the questioner really wanted to know about all people in (a) or (b), and the student could have included people in (a) but did not.
There is not really enough context to know whether the questioner would be satisfied with the answer given. That's why we have conversations that go beyond one question and answer. ;-)
As for a fill-in-the-blank answer, the teacher was no doubt looking for a response that uses the same tense: have worked. I have been working might well be an indication that the student missed the generality of the question, i.e., did not realize that s?he could include people with whom s?he no longer works.