Theory:Doctor Who television discontinuity and plot holes/Into the Dalek


 * The Doctor comes onto the Aristotle. First they consider killing him. Then, even when they decide he might be useful as a doctor, they still keep him under armed guard "in case he's a spy". But somehow they let him pop off in the Tardis for a few minutes to pick up Clara?!
 * The Doctor has dealt with soldiery types before with UNIT and all that so he must have found some way to get them to back off - smart-mouth retorts and mind games, and stuff like that that just generally confuses other people. And it wouldn't be the first time he's slipped away without anyone noticing, in this case allowing him to pop off and pick up Clara.