In your situation, I think that “Did he call in on you?” could mean one of two things.
1) To call in on = to meet. The IT person was wondering if your boss met you to discuss this issue.
2) To call in = to report by telephone; on = with regard to. The IT person wondered if the purpose of your boss’s calling was to resolve the same issue you were mentioning.
It is most likely that 2) applies to your case.
To tell on someone = to let out secrets about someone. It does not seem relevant.