'Twas the exigencies of early color TV. The TOS cast wore primary colors: red, blue, yellow (okay, a sort of yellow-green that's termed "heather"). Nothing to get hung up upon, and for all we know most non-human crew were color blind, or read both "red" uniforms in different ways. For example, maybe engineering red looked very different from security red in ultra-violet.
Human eyes are not the only eyes in Starfleet.