What the previous post refers to is the fact that, if you didn't complete the first Mission first, you can never get 100%.
Otherwise, the game is not wrong. If you won the first Mission first, then you are left with finding a missing race or Championship. A Bronze cup can look like a Gold one, too. You may have finished all races in a Championship, but you may have missed doing the Championship series itself. There are lots of ways you may have missed something. Keep digging.
Cheers,
MasterGT