Lately I too have been collecting rares in various breeds. One issue I have is that I will already have 3 of a given pet and need to drop the uncommon pet to capture the rare version. Alas you currently can't do that once you start a fight. I am looking forward to 5.2 where I can forfeit, drop the uncommon, and redo the fight.
There have also been times I have my "leveling" team and not my "capture" team (with a Terrible Turnip) and will accidentally kill the pet I want to capture