Does "excuse you" imply I'm at fault?
Solution 1:
Excuse you is the subverted form of the idiom excuse me. It definitely implies that it was your, i.e., the non-speaker's, fault.
If you do something rude and minor (like burp, or accidentally bump into someone, etc), you say "Excuse me" to apologize.
Some people rudely say "excuse you" to someone they feel needs to apologize for being rude. For example, if the husband burps and does not excuse himself, the wife may say "excuse you!" This is a sarcastic and very unpleasant expression.
wordreference: excuse you
If he was joking, that would be the joke. It would only be funny if it couldn't possibly be your fault, yet he's saying it is anyway.
Whether he was joking is impossible to tell if you don't tell us how he said it or if he smiled.
Solution 2:
Without knowing your culture, let me assume that you are an American. Then the meaning of "Excuse you" depends entirely on the speaker's tone of voice, facial expression and body language.
If the speaker is smiling, "Excuse you" is a sort of joke, an ironic figure of speech. It recognizes that neither of you is at fault and it's the sort of thing that happens all the time. There is even a famous comic strip Alphonse and Gaston which plays on the situation. In this case, it is assumed that both of you share the joke.
On the other hand, if the speaker is not smiling, and speaks brusquely, the presumption is that he feels that his higher status requires that you get out of his way.