Assuming you had 198 BP at the End of Chapter 2/Before passing the checkpoint... I'm looking at my handwritten notes that has all BP and Books and here are some suspects I have:
Temp Librarian Plus 1-3. All Hidden Quests available sequentially after you complete the Mission Board's Temp Librarian Quest (So return the initial quest, can get Temp Librarian Plus, get that book and return it, get Temp Libraian Plus 2...). Each one sends you to a far off place to get a book. Elmo's Inn, the Stone Pillars on that one field, and Sanktheim Gate. Collectively these would amount to 11 BP (3+4+4).
Any other scenario will require a more complicated combination which also probably makes it less likely to be the culprit but: Disarming all the smoke in Zeiss Central Factory when it's attacked adds up to +5. Getting into any encounters during Leiston Fortress incurs a penalty (you start at the Max Bonus and it's -1 for each non-mandatory encounter you get in until you deplete all the bonus BP. Once you find the stalled truck from the regular mission board there's a hidden quest where you resolve it by backtracking to Zeiss and find the part need for the repair that's worth 5 BP. There's another +4 Bonus for the quest where you get the right gift for the guard's girlfriend.
I'm thinking your problem was the Temp Librarian Plus series because taking a quick glance at the guide you mention they are brought up but because the nature of those quests require a lot of backtracking to and from Zeiss, if you end up forgetting about it when you return the original non-hidden board quest you're screwed.
If you have a save before infiltrating Leiston you can try seeing if it's still available if it's bothering you.
But the answer to this is a resounding no.
FC is the one game where you're allowed to miss a boatload of BP and still reach the max rank. You can miss a downright silly amount of BP in FC. Like 80 or something. I don't think there's any difference in FC between reaching the top rank and having perfect BP. You do get a Luck Quartz for having perfect BP transferred over into Sky SC but that's not a dealbreaker whatsoever.