I would probably look at your Video Options (in-game under Options) and see what your Brightness and Gamma levels are in-game and lower them.
I don't know if you play Klingon vs Klingon PVP, but I am gonna assume you play Fed vs Klingon PvP. For me, the colors are Green (Fed) and Orange/Yellow/Ochre (Klingon). It does sound like your settings need adjustment, at least in-game.
Klingon on Klingon ground,and space pvp is yellow, and a mustard. Then your team is a white/grey. Standard blue / red would be great especially as it still counts the match as red vs blue... Still have to watch the bar when i die to see if I'm a yellow red team, or a mustard blue, or mustard red... etc..