I am sorry to hear about the problems you had, however, it is on the site. There is a section that says. What documents do I need. At the online check in point there is even a place for you to look. There is another place that says Are Passports required and it explains that visas may be needed. So it actually spelled out for the customer several times.
However... I would also agree that the online check in should have a place that asks for the Visa information, just after Passport #.
I wish you luck and hope you find some solution to your problem