In the opening scene the windows of the first floor in Dr. Pretorious' house are shattered. A little later in the movie, when the team arrives again at the "crime scene", it is clearly visible, that the window classes are still unbroken.
When Crawford tries to get out of the van, he can't. Bubba mentions child proof locks. Shortly after that, Bubba gets out of the van using the same door, with no problems.
When Crawford first tests the machine for Katherine and Bubba, it is obviously still night time, but a short time later when he turns it off there are rays of sunshine pouring through the window as if it is late morning.
The wound on Crawford's face changes from the left side to the right side several times throughout the movie.
For the entire movie, the characters all mispronounce "pineal," making it rhyme with "vinyl." It should rhyme with "finial."
The Pineal Gland is a backwards facing part of the brain, like the cerebellum. In order for it to project through the front of the brain and out of the forehead on a stalk, it would have to destroy a lot of important stuff that would be in the way.
When Bubba is knocked down and strikes the back of his head, cushioning on the edge of a table (to protect the actor) can be seen in one angle, but not the other.
When Bubba tackles Crawford down the stairs, the body makeup of the stunt man smears along the wall.
When Bubba tackles Crawford and they fall down the stairs, for a brief moment just before they hit the landing "Bubba's" face is shown (from the camera at the top of the stairs), and it is obviously a stunt double.
You can hear the sound of the light switch flicking before Dr. Katherine McMichaels switches the light switch on and off in the house of Dr. Edward Pretorius.
When Katharine is in the institution for the first time, and she is looking through the windows on the cell-doors, the audio of the man who screams at her does not match with the movement of his lips.
After Dr. Katherine McMichaels sprays the machine with a fire extinguisher and it turns back on a puppeteer's leg, the rig holding up the Dr. Edward Pretorius monster puppet can be seen behind the puppet.