I think it's probably contextual. Mainly, I'd interpret the phrase by accompanying facial expression... for example, if someone looked annoyed/disgusted then I'd probably go for an interpretation of the 'something wrong with it' type, whereas if they looked mildly confused I'd interpret it as "I just don't see where the humour is in that".

Fair point. In the context in which it bit me this morning, I was saying it on-line, so there wasn't an accompanying facial expression to clarify what I meant...