Other mistake: An agent and Scully analyze the fragment taken out from Duane Berry's body. The agent draws Scully's attention to "small markings", which are half a monitor size, and Scully naively asks where they are.
Continuity mistake: When the Smoking Man brings the alien fetus to the Pentagon storage facility, he places it on the second rack, then in the next shot he walks away from the rack situated in the middle of the corridor.
Revealing mistake: In the beginning of the episode two frogmen jump into the water from the boat. The boat is supposedly out in the Pacific Ocean, but in the lower left corner you can see a harbor in the background.