It appears I'm the first person to discover this wierd Bonus exploit.
On board 12-1, there is a way to easily get all 9 bonuses, which I'm sure most of you know, but what you probally don't know, is there's a way to raise the Bonus rank from 17-19 to a solid 21.
Seeing how It's easy to get all 9 ranks, I decided to use a old school tactic(the ol, reload save endlessly until you get the desired options).
Well this is how it went(Note: The first time I watched the story, but after that I just kept skipping it for speed) "Enter stage, look at bonus, hit Quit command, reload, and repeat like 4 times". The bonus of the stage should read rank 21 now, and the bonuses are indeed the increased rank as well.
PS. I checked to make sure, Its not in the strategy book of the game, nor is it listed on gamefaqs