The Phoenix Saga (4): The Starjammers - S3-E6
Plot hole: Corsair takes out the X-Men by having Raza calibrating their stun weapon to humans. Since Corsair is also a human, the blast renders him unconscious along with the X-Men, and the Starjammers take him away. When Wolverine and Phoenix regain consciousness, they realize that Cyclops has been taken by the Starjammers as well. The problem is since Corsair was unconscious, he couldn't have possibly ordered the Starjammers to take Cyclops with them, and the Starjammers had no reason to take Cyclops of their own volition. Raza even acknowledges that Corsair is the one that takes Cyclops. (00:08:15 - 00:09:00)
Suggested correction: His plan was always to blow a hole in the tube to have a train crash at that location. This would have caused mayhem and take up a lot of resources (police/ambulance/fire). Bond chasing him had no impact on this part of the plan. Then when his team picked him up, his team would have known where M would have been on that day and would have driven him there. With resources on high at the train crash site, it would have made it easier to reach M.
XIII
This aspect is a bit of a plot hole for me too - one of the factors outside Silva's control is when he can escape MI6 custody, which depends on when Q triggers the 'Granborough' Trojan, which Q only spots with a bit of help from Bond. That triggering could have been hours, days, weeks or never - pretty fraught with risk to rely on individual(s) making that happen at a plot-convenient moment... otherwise Silva has a bunch of associates hanging around London for a few days permanently on a few minutes alert for a random event.