Only time this has happened to me is when I have entered my passport number wrong. I've been using my passport for six years and a few weeks ago went to put the number in for online check-in and I swore I was putting it in right. Well, turns out my brain wasn't working correctly that day and I had transposed a couple numbers. So I'd say triple check you're inputting it right. Otherwise, maybe call AA and have them put it in?