(Around 48 minutes) Tim Shaw is standing behind Karl when he takes one step towards the Doctor but in the long shot he is much further in front of Karl than one step could have taken him.
(Around 24 minutes) when the explosion goes off, Ryan turns sideways to grab his Nan, but in the next shot he is facing forwards with his Nan behind him.
The initial passing shot of the train that Rose, Graham and Karl are riding in, shows carriages with windows with horizontal cross bars. The train is also being pulled by a separate locomotive.
All the following internal train shots show windows that have a single solid glass pane. The driver is shown located at the front of the train and not in the separate locomotive.
(Around 47 minutes) the crane has a bar across the end which the Doctor would have hit when she jumped to the other crane. It disappears when her foot leaves the crane but reappears when she is flying through the air.
There is a moment after the gang first discover the murdered and mutilated man where everyone is looking rather disgusted and uncomfortable, then as the shot changes to behind the Doctor it is clear that she is no longer speaking, as there is no change in her body posture, breathing or motion of her jaw, yet we hear her still loudly talking, saying sorry to everyone for seeing this, as well as apologising for a few other things, making it obvious that these lines were dubbed on later to try to 'temper' the discomfort of the scene.
The Doctor has a funny turn then declares that she has formatted Ryan's phone, Ryan protests, but she says 'Come on then!' and runs off following some kind of detector device that has appeared on the phone. No explanation is given.
When Ryan encounters the strange light in the forest, he has the red device in his hand, which the Doctor then threatens to blow up. When did it come into Ryan's hands? When he went down to the forest, he didn't have it with him, the viewer does not see him picking it up from the ground.