Plot hole I just realized regarding to Catherine, any explanation?

Before the events of the actual game, Catherine and her team previously tried to launch the ARK, I assume they all copied their minds onto the ARK before trying to launch it, why wouldn't they?

At the end of the game Catherine was once again uploaded onto the ARK, so now is there 2 Catherine on the ARK? One being the human Catherine that was copied before she died, and the other being AI Catherine uploaded at the end of the game, both with separate memories of what happened?

And before someone says that they would've uploaded when they launched, wouldn't they have ran into the same problem where no one would be left behind to launch it as we did in the game?

Also, why did Simon not "fall asleep" during the brain scan at the launch as he did when he switched suits?