If you have a Vengeance mode ready and a mission (mode) ready and drain, you won’t be able to start a mission before your next plunge. You’ll have to shoot either mission start shot to start it.
This is why it’s a bad idea to use the Punch It torpedos maniacally as the ball is draining if you’re no longer in a mission.
IMHO, this behavior constitutes a bug, and used to confuse the crap out of my players. If a mission weren’t startable in this situation, I’d say it’s working logically and as intended. The fact that you can shoot an extra shot and start the mission makes the whole thing just stupid.