Before the snap. A makes a false start. B has twelve men in the formation.

How and who do you penalize?

Canadian Ruling
 

The Cdn. equiv would be:

Before the snap, A commits illegal procedure. B has thirteen men in the formation.

How and who do you penalize?

Ruling: Since there was no snap due to the dead-ball illegal procedure flag, there is no foul for illegal substitution (too many men) on B.

5 yards, down repeated.

NF rules.

Rule 3-7-2 says in part that "replaced players must leave the field immediately." If B actually got into their formation with 12 people (and I heard about a subvarsity game with a female player, so I'd better said "people"), then someone did not leave "immediately." That being said, this was a foul before the FS, so I would penalize the illegal substitution.

I can't see any situation where you have fouls on both. You have to decide - did B have 12 out there illegally (someone didn't leave immediately when substituted for) - if so, you flag them. If B had 12 out there, but one was still leaving, there was no legal snap - so you have False start on A.

Sounds like, in this situation, since you say "12 in the formation", that you have an immediate foul there on defense for illegal substitute, and the false start never really happened.