8 Skulls or 9?
In the beginning of film, there is a scene where all the new Skull recruits are in coffins. If you are to count the coffins, you'll notice there are 9. To back this up, Lucas' friend Will asks "if Caleb Mandrake and your 7 new friends walk in, will you talk to me or them?". Lucas + Caleb + 7 others = 9. Later the Skulls are put together as soul-mates in pairs. How can 9 people be put into soul-mate pairs? After the skulls are put into pairs there are no longer 9 skulls in the movie, but eight.
Impossible Coffee Run
In the scene where Joshua Jackson's character is taken from the mental institution by his girlfriend, and they go to a hotel, notice that they are sitting on the bed drinking coffee. The cups, however, are from "The Coffee Bean" and "Tea Leaf", a California-based coffee house. The movie takes place on the EAST coast.
Branding Appears & Disappears
When Lucas and Chloe are in the hotel room, after escaping from the University Provost, they are researching on how to "defeat" the skulls system. Lucas is pacing back and forth in the hotel room and there are several shots where he is seen through the reflection in the mirror. If you look closely on his wrist, the skulls brand appears and disappears randomly.