(at around 1h 12 mins) When they're watching the tapes backwards, they see Tristen hiding the tapes under some rocks (where they found them). The tape they're watching is one of the tapes they found, but when she hid them, she was being recorded on that tape.
(at around 41 mins) When Erica is talking to Stephen about how tense he is, he bangs the table and knocks the cup in front of him over. In the next shot, the cup is standing up again.
(at around 11 mins) When Kim asks Tristen about how pregnant she is, in wide shots Tristen has a wisp of hair sticking out at her left, but in close shots, she doesn't.
(at around 8 mins) When the tour group meets Kim in the cemetery, she is lying on a grave with the name "Treacle" written on the headstone, but when they move past the the headstone and see it from the other side, it clearly has the name "Further" written on it, and also looks much older. (This is due to an extra on the DVD version, which includes watching a section backwards to look for clues. These clues then point you to different parts of the film to solve a puzzle, the tombstone is part of that. There is also a shadow of a tombstone that appears as a cross and then just a normal tombstone, and also ghost images throughout the film.)
(at around 25 mins) When the group wakes up to all the torn up paper covering their campsite, the files and papers that Tristen holds continually changes position, amount, etc.
After Tristan has her miscarriage, the nurse tells her that she's not only lost a lot of blood, but more than usual. She finishes by saying, "It's for the best, your body's telling you something's wrong." A nurse would not say this. Even if Tristan did have something wrong, a nurse would be very sympathetic toward her and offer her condolences. She would not say that a miscarriage was for the best. Also, even if this nurse was a "plant" by the Blair Witch as a mind game, this statement would not be said.
(at around 47 mins) After Kim gets her beer from the store refrigerator, a woman comes round the corner and bashes her trolley into her. However if you look in the glass of the door behind Kim as she gets her beer, you can see the reflection of the woman standing there and waiting for her cue to push her trolley round into Kim.
(at around 53 mins) When Jeff lifts his shirt to reveal the symbols on his stomach, the actors stomach hair has obviously been shaved to make room for the symbols.
Next to the front door of the factory there are several Maryland license plates hanging on the wall. All the plates are the same.
This is obviously just a license plate collection.
(at around 5 mins) The opening scene of the movie is set in Autumn 1999. The stereo in the van is blasting Marilyn Manson's "Disposable Teens", which was not released until November 2000.
(at around 1h 7 mins) When Jeffrey answers the door to his house and the dogs are barking on the other side of the broken walkway/bridge a thin wire can be seen attached to a dog to keep it from falling.
The movie's action is set in Burkittsville, MD, which is in Frederick County, but at the end the characters are seen being hustled into what is clearly labeled the "Howard County Courthouse," which is located in Ellicott City, MD, nowhere near Burkittsville.
Even taking into account that this was possibly another of the Blair Witch's mind games, the surveillance video of Jeff hiding Erica's body in the closet could not have happened. It is well established that he was in the loft the whole time studying the video footage of the night they blacked out. There weren't any scenes of him being absent for a period of time that could explain it.