After playing with various pieces on a Romulans and Klingons, my hypothesis its that items with the wrong number of color options are causing the weird linking. Like changing a belt color changes your shirt, or a helmet your shoulder pads.
The common demomitor is that one (maybe) both items have too many (or maybe not enough) color options.
This is the color options you change and it does nothing because there is nothing to color. So when you change the color that does work, it also changes the color of another item.
Example:
Klingon Honor Guard Helmet. Has 3 color options. #1 and #2 do nothing. #3 colors the helmet. But then also changes the color of part of your shoulder pads.
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Comments
Just click randomize, then reset everything manually to effectively work-around the issue and un-link all the colors. BUT, you've stumbled upon a larger issue: Devas, LIBERATE THE COLOR PALETTES! FREE THE SPECTRUM! RAINBOWS = DIVERSITY! I want canon colored TOS uniforms, dammit! I want my avacado command shirt and Motion Picture pastels. Stop arbitrarily limiting color choices to ugly non-canon selections! And just turn off all linking. It's pointless! How hard could such alterations be, and yet directly result in a MUCH higher quality game? Mind-boggling! Just do it! Because we love you dearly.