This seems like an odd one but it has happened to me twice now. Both were on my Jedi characters, my Knight/Sentinel and my Consular/Sage. My Knight's eyes were set to blue, but were later green, which was immediately noticeable during the first cutscene. This was last year, and didn't think much of it, he doesn't look terrible with green eyes. When I made my Consular, I gave her green eyes, but her eyes were brown. I was kind of off-put by it and changed it at the cartel bazaar.
Not the biggest deal, considering it's only twenty coins to a subscriber, but I'm extremely sure it wasn't an accident, I lock my customization options after selecting one, and sometimes even write down the appearance options in case I decide to delete the character but want its appearance.
Very odd, but I figured that if it's something BioWare can fix (seems like a simple bug to me, but I'm not a programmer), I might as well try to bring it to their attention. May the Force be with you