I have this problem before. It was because my travel agent put my birthdate in incorrect (by one day). Once I got to the airport, no biggie, they checked my passport and issued a boarding pass.
Sometime I have trouble checking in online as well as my travel agent puts MS after my name and it seems to confuse the system. Once again at the airport never an issue.
As said above, just give yourself enough time to check in at the airport.