User blog comment:Suparockr/List of Plotholes throughout the series/@comment-4950455-20120729072851/@comment-1679409-20120729160517

My possible explanation is that human different fleets and flotillas have their own color scheme or at least did in the first game. After that, there may have been an effort to standardize color schemes to keep down the confusion (i.e., "Okay, turians, you can have red. We'll take blue.  Asari can be purple...").