Among everything that Sean caused to malfunction, it's never explained how Sean was able to manipulate the film reels/computer system to cause the projection to go haywire on the one movie and the lights to malfunction on the other. As Merle stated, he couldn't find anything wrong when he was examining the issue with "Cut to Black" but only that everything was on a computer nowadays.
On both occasions when Sean disappears, he is found tied up with his hands bound, first with rope and then with handcuffs. This would have been impossible since he was working alone.