Continuity: Doggett says that Mulder and Scully first met Gibson Praise in 1997. As we saw in the season 5 finale "The End," Mulder and Scully first met Gibson Praise in 1998.

Continuity: When Scully points out the location of the last time they saw Gibson Praise, she points to the (real) Palo Verde Nuclear Plant, which is west of Phoenix. In 'The Beginning' the plant shown was the (fictional) Rolling Hills Nuclear Plant, 60 miles east of Phoenix.

Continuity: When Martin takes out the nanny-cam from the bear, the lens-protection is on so the camera could not have recorded anything.

Continuity: When Ray is eating the sandwich, there is a large bite out of one corner just before he removes the foil. In the shot from behind after the foil is removed, the bite is only from one slice of the bread.

Continuity: Just before he removes it, the foil disappears from Ray's sandwich in one shot, then appears again in the next shot.