Yes, the script was a mess. And that comes from somebody who loves Moffat. I wonder how much his draft was altered, because this is exactly the opposite of what I expect from him. The man is pretty much a genius and knows how to attack genre fare - I would think this would be right up his alley. I'm guessing his vision was distorted at some point in the film-making process, either by the other writers or by Spielberg.
Most, if not all, of Moffat's draft was rewritten by Wright and Cornish