Continuity mistake: When Bill Murray is talking to the dead guy in the chair, the dead guy's eyes are open. But from a side shot, they are closed. (00:33:00)
Revealing mistake: During the opening scene, a few shots after we see the Outworld ninjas falling through the portal and leaping about, there's a shot of several monks fleeing that tilts up towards the (digitally replaced) sky. As it does this, you can see several hard lines about in the sky from where pieces of the digital animated skies were "stitched together." It's easy to miss the first time, but if you know to look for them, they're pretty obvious. You can see similar lines in the sky in several other shots throughout the scene, but it's most noticeable here.
Continuity mistake: When Barry tells Ray to go check if the fisherman is alive, Barry's flashlight keeps changing position from his right hand to his left hand. (00:15:58)
Continuity mistake: Talking with the feds about the case, Cross says "This guy's a collector." Kyle Craig in the background goes from holding a pad to a folder, and then closes it multiple times when it was closed to begin with. (00:24:00)
Continuity mistake: When the medical examiner notices that there's something wrong with the brain of the corpse that she is examining, she's making a gesture with her hands but in the next shot she has them by her sides. (00:30:39)