Early on, Catie gives Pete an unwrapped candy cane. He even licks it. Towards the end when Pete returns to the world that he knows, the candy cane appears within an unbroken plastic wrapper.
Alternate Claudia states several times that she wants to access the Warehouse to retrieve the Rheticus compass and free Joshua from the dimensional vortex; however, that artifact was actually trapped with Joshua in its original appearance.
Pete tells Myka she was the one to smuggle H.G. Wells out of the Warehouse through the hidden exit, when in fact it was MacPherson who smuggled her.
After Pete knocks out the agent, he rifles through the agent's pocket for the keys to the cuffs and it is obvious that the cuffs are not actually completely on him. In the next shot, he uses the key to unlock the cuffs that are now locked.
The computer screen that McPearson is looking at changes. It says 520 items listed and on the right there is a stocking but in the next scene it now says 342 and on the right is a picture of a flower.
Pete sits on the long candy cane kept in his back pants pocket. Astoundingly, it comes out unbroken.
Alternate Artie says that MacPherson convinced the regents he had been rehabilitated, which means he had still been burned as an agent in this reality, and thus he would have still been given the injection that makes his blood corrosive enough to burn through his veins should he enter the Warehouse without wearing the crystal necklace artifact to counteract the effects of the injection, however he is shown to not be wearing it and is somehow fine.