Other mistake: When Omega Red brings the nuclear submarine to launch depth, the underwater cliff he parks it on is the exact same cliff where the submarine was originally located. (00:03:30 - 00:15:10)
Other mistake: After Omega Red stabilizes the nuclear sub while it is moving, the military somehow has a live video feed from outside the sub despite the fact that they didn't send any other submarines out to monitor the mission. (00:09:00)