How can I handle this?

[MJT]

There are some serious problems with this situation, and it is the referee, not you! He is undermining you, which is WRONG! He is making the "new guy" look bad, which is WRONG! He is not helping you learn how to improve, which is WRONG! By picking up "your" flags, and telling the coach what he did, he is trying to build himself up while taking you down, and I don't know what he could do that would be worse than that.
I would not work with him ever again. I would copy all these replies, which say what he did is wrong, and send them to him so he can what an idiot he has been.
Safety issues need to be called no matter the time left on the clock or the location of the field. BIB, clips, PF's need to be called and one official should never be upset when you call those.