It's a recurring issue for me that I can't completely remember a saying. In this case I think I've heard someone using something like:
I've interrogated him and he seems to have an alibi. Something still bites me, though.
So the meaning is like 'still having a suspicion about something/someone' or 'something is still bothering'.
Am I making this up or am I confusing it with a very similar phrase? If not I'd be interested to hear more usage examples.