Sometimes in the character creator, the colors of seperate clothing parts seem to link together.
For example; I try to change the color of 1 part of a Klingon shoulder pad and it changes the same part of both pads, part of the torso armor and the belt at the same time. Fed ones have a habit of belt/glove/scarf combos.
How can you use the canon outfits you want if it won't allow the right colors?
Seems to happen a lot on my KDF character's female Orion bridge officers. Change 1 color and all colors top to bottom in that column will change to the color I chose. Only way I found around it is while in the third window where you pick your outfit pieces, click Randomize at the bottom a few times. This will change your costume only and not your hair or facial features or anything, then choose the various outfit pieces and try changing the colors. Doesn't always work though.
Supposedly they "fixed" this a few weeks ago. I remember something in the patch notes about it. Don't remember which patch though.