Revealing mistake: In the overhead shot of Gordon waiting for Spencer at Knapford Station, you can see that the bushes on the far left track aren't rendered properly, as they appear to overlap the rails.
Continuity mistake: In the scene where Percy is talking to Stephen, Thomas reverses down the track he has arrived on and stops. But when Percy leaves, Thomas has mysteriously disappeared. Also, the track Thomas was on ends at some buffers behind him and leads to the turntable in front of him, but that was set to Percy's line.
Plot hole: Emily begins to pull Henry out of the shed, but however there is no track leading to the other end. Also, the turntable is not big enough for both engines to fit on.
Other mistake: It is impossible for Gordon, Edward, and Toby to all puff into the Sodor Steamworks at the same exact time, as there is only one transfer table there.