Well, I'd say that in this instance you should trust your boyfriend. He may be lying (or maybe he isn't) but why would you take the word of his ex over his? You asked and he said it didn't happen.
She is clearly somebody with a vested interest, whether its pure hatred or just total assholery. The point is she's a biased individual here who might still want him. Now, I'd make sure you let him know that he is not not deal with her at all: no texting, calling, visiting, seeing, hanging out, etc. He should understand and respect this given that this chick is clearly trying to break up your relationship.
So, at the end of the day, fool you once, shame on them...you just have to believe him. But if something happens that gives you any suspicion..well, then dump him with the quickness!