Agent Mulder signs his resignation, but his signature is totally different from the signature on his badge in the intro.
The date (January 3, 1994) on Scully's medical charts when Frohike looks at them is at odds with the recent continuity. In Duane Barry (1994), on-screen titles establish Scully disappeared in early August, with a subsequent episode 3 (1994) being set sometime in November.
Capt. Scully is wearing US Navy Dress Whites with the coat tucked into his trousers. The coat is worn on the outside, not tucked in.
A Bible verse is inscribed on the tombstone. It says, "The Spirit is the Truth," and cites it as "1 John 5:07." The verse is actually 1 John 5:6.