Could be that he simply thought it weird that she didn't realize what their, uh, relationship was.
Or simply it's something he says when he's got nothing else. You guys mentioned he said the phrase more than once throughout the movie. Sounds like it may just be his...dead air filler.
Can't you see the scenario where McCoy left something in the fridge and finds it missing. Turning to Kirk he says, "My brandy is missing!" And Kirk just shrugs saying, "That's so weird."
