In the opening scene in his office, Mulder tosses a pencil that sticks in the "I Want to Believe" poster. At that point, a total of six pencils may be seen sticking out of the poster, including the one he just threw, which is directly below the flying saucer. When Mulder gets up to remove all the pencils a moment later, there are seven total pencils: one above the right side of the saucer where there was none to be seen before (although there were a bunch of holes at that spot in the poster in the earlier shot), and none directly below the saucer where we just saw him toss and stick one.
After Guy Mann leaves Mulder in the cemetery, Mulder pulls out a bottle of bourbon and opens it...the label is facing him. When he puts it to his mouth to sip, the label faces out.
At the beginning, we see Mulder throwing pencils into the "I Want To Believe" poster and clearly see one in the letter N in Want...When he removes them, there is not even a hole in the letter N.
When Pasha sneaks up on Mulder between the two tractor trailers Mulder spins round with his phone's camera app still malfunctioning. As he does this we first see the phone's screen facing Pasha (meaning that the flash side is facing Mulder, effectively taking pictures of himself instead) but when the scene cuts back to Mulder the screen is now facing Mulder once again as it should be. Moments later once the Were-Monster appears this happens again as Mulder and Pasha turn to face it, first the screen is facing the Were-Monster and then when ti cuts back to Mulder the screen is now facing him again.
When Scully and Mulder are examining the body in the morgue, his eyes are clearly moving below his closed eyelids.