I don't know what his problem is. You should have asked him, あなたは中国人ですか? and ask him if that is better.
Probably the lady didn't think twice about it. Obviously you're a learner of Japanese and won't know the most natural ways to speak.
I'm just guessing but perhaps he thinks it's insulting to question somebody's nationality. Maybe he thinks it's implying that they might not be Japanese or not look Japanese even though they are?
That being said, it's probably more natural and safe to say something like 出身はなんですか?