One of the characters says that the exodus (to Terra Nova) would take 24 hours. Episode 1.11 had already stated that Operation Exodus phase 3 would take 48 hours. (Note: The evacuation time would be different for each planet, depending on the distance between each planet and the moon).
It is impossible to have two bodies (spacecraft, Moons, whatever) in the same orbit and one going faster. If one Moon was, it would have to be in a different orbit, most likely in lower orbit. (Note: several mysterious occurrences take place in this episode otherwise deemed impossible, such as Regina having two brains as well as the basic premise of the moon returning to Earth's orbit - so the two moons' differing velocities in orbit should not be deemed impossible within the episode's context).
As Koenig and Carter enter the crashed eagle on the alternate moon, as they head towards the cockpit of the crashed eagle the number on the door at the rear of the cabin has 3 stenciled on it. As they approach the cockpit had the number 1 on the door. Throughout the series, non-matching numbers on the door is more far more common than matching ones, so there's no reason to assume that they should match.
As Koenig and Carter enter the crashed eagle on the alternate moon, as they head towards the cockpit of the crashed eagle the number on the door at the rear of the cabin has 3 stenciled on it. As they approach the cockpit had the number 6 on the door.
Regina's belief that she and Alan are married in her perceived reality makes no sense. She never appeared in any previous episode, and in this one, there is absolutely no established connection between her and Alan. To him, she's just another random Alphan. (Note: After the duplicate moon was created, it was sent through a time warp, arriving at Earth five years ahead of the original moon. One of the episode's plot points involved Regina having a psychic connection with her duplicate on Earth, who was married to Carter. Her reality was blurred in between being on Alpha and being her "other self" on Earth).
In the teaser, the moon is subjected to extreme forces before it goes through the warp. In Main Mission, a man on the upper level falls to the deck below like a sack of potatoes, without the slightest reflexive attempt to catch himself.