Continuity mistake: In the opening scene, Tom stands outside the General Store, and walks into it, through a door that is already open. However, in the next shot, from inside the store, both shop doors are still closed and Tom has to open them.
Continuity mistake: When Tom gets a copy of his hospital admission records, his SSN is stated to be 542-68-4360. However, in an earlier episode ("A Rough Whimper of Insanity"), he tells the hacker that his SSN is 549-24-1889.
Stay Tuned - S1-E17
Continuity mistake: When Tom and the English teacher walk into the campaign HQ, a shot is shown of a security guard glancing up the stairs, and a blonde woman carrying a poster walking past. After Tom and the teacher have finished having a conversation with a balding man wearing glasses, the exact same shot is shown again.
It's Not Such a Wonderful Life - S1-E12
Continuity mistake: In the previous episode, Tom was shot and had a scar from the resulting bullet wound. In this episode, when he takes his shirt off on Christmas Eve while talking to Alison, the scar tissue has completely vanished. Bullet wound scar tissue - even after years - doesn't completely vanish. It's been less than months since the previous episode.
Continuity mistake: When Tom and the girl get back from the dance, they go into the sitting room to see that there is a roaring fire already going, with the stove door open and a whole log on the fire that's barely been touched. The fire is too high and the log too untouched to have been burning before Tom and the girl left to go to the dance, and there's no one else in the house to have started it before Tom and the girl arrive home and open the door to the sitting room.
Continuity mistake: When Tom initially breaks into his studio, the "Hidden Agenda" photograph has a plaque underneath it. When he returns later with Dr. Bellamy, the plaque has disappeared.
Through a Lens Darkly - S1-E20
Continuity mistake: At the end of the episode, Tom is absolutely drenched because the car has crashed into a river, and he has to wade through the river to get to the riverbank. However, as he walks away, he doesn't leave a single wet or muddy footprint behind him despite this.
Through a Lens Darkly - S1-E20
Continuity mistake: When Tom lifts up the girl's sweater (with both hands), he is still wearing his shirt. In the very next shot, he has magically lost his shirt too, even though his hands aren't free to take it off, and the girl wouldn't have had time to do so in the space of 1 second.