The ark is shown falling into a certain angle. When they entered it you can see the doors and floors are straight.
Sue looks at the hologram and says that the children have been moved "sixty miles" from their previous position. But if the path shown in the hologram represents sixty miles, then the five children are currently positioned miles from each other. This is even more implausible considering that the children's trackers have been removed from their bodies and are all together in one little packet.
Mother visits a memory of her past and she sees herself strapped to a seat while her breasts are bare; they're depicted without any nipples, yet, they're clearly visible through her shirt on several occasions when in the present.