There is no penalty for having 12 men on the field. There are two different situations that exist when a replaced player doesn't leave as required:
ILLEGAL SUBSTITUION
When a substitue enters the field and notifies the replaced player, he has 3 seconds to start leaving the field. It has nothing to do with a huddle or how long it actually takes him to leave the field after he starts off. Obviously, if he doesn't get off before the ball is snapped, it's a penalty. If the snap is imminent and the team does not realize there are more than 11 players involved, then we are to flag it before the snap.
ILLEGAL PARTICIPATION
If a 12th player participates in the play, it's illegal participation. We try to count before the snap but during hurry-up or when players run onto the field at the last second (Tennessee @ KSU), so that a team gets a 5 yard penalty and avoids the 15 yarder but it's not always possible to flag them and kill the play.
This post was edited on 11/22 9:03 AM by FBRef