Corrected entry: It's unreasonable to assume that Sarah couldn't have found that PAT's configurations had been changed. Ben had DELETED some of them even, and it would have been a red flag if he had only DISABLED them, so for Sarah to overlook this is only convenient to the plot, and something she easily should have been able to detect.
Corrected entry: When Angie gets her hand scanned by PAT. PAT is able to tell her age, illnesses, injuries and if she has broken bones. Sara explains it uses a DNA sample for these tests. DNA samples do not hold this kind of information.