Factual error: Proteus refills its air supply in the lungs. The lungs are filled with normal sized oxygen molecules. How are they supposed to breathe them? (In the book, they had a miniaturizer on the sub, but there is nothing in the movie to explain this.)
Factual error: The Dalek mine is set in Bedfordshire. We see the encampment with high mountains beyond. Bedfordshire is a county of low rolling hills, with virtually no rock.