My biggest peeve with Chrome on OS X is the nonstandard behavior for clicking on the Omnibar. Normally, a single click places the caret, double clicking selects the word, and triple clicking selects the whole field. Chrome reverses this for its bar, and it's jarring me every time I do it. While they explain why they did it, it feels 'wrong' that the majority of the Mac users commenting on the issue [1] were against it, but the UI design team felt it was better.

[1] http://code.google.com/p/chromium/issues/detail?id=24349