How do you say "Do you like green or yellow?" In other words, if you're not asking for a choice, just yes/no.
"Do you like green or yellow?" is literally "Máš rád/ráda zelenou nebo žlutou?" Technically you can answer with yes/no, but many people consider such answer insufficient or even rude.
If you want yes/no answer, you have to ask only one color. "Máš rád/a zelenou?" - for green color; Máš rád/a žlutou?" - for yellow color.
Although my initial response would have been "Do you prefer green or yellow," and not realizing that you'd already been there, I answered (experimentally) with "do you like green or yellow better" which, as you've pointed out, was not accepted. In case it's just a missing translation, I've reported it.