Around 9:00 Mulder and Scully enter the Right Hand compound through a gate in a chain link fence. They are chased by dogs and run back to the gate. In one edit the fence is completely open; in the next edit the fence is closed, and only the gate is open.
When Mulder is talking with Skinner via earphones, in a close-up, Skinner has his hand on his ear and is talking to Mulder. In the shot after that, Mulder is talking back. Skinner in seen in the background, silent and with his hand no where near his ear. In the next shot, however, he got his hand back on his ear again.
MacDougal's driver, PFC Burkholder, is missing the US Army Service Ribbon on his Class A uniform. As an enlisted man, he would be given the ribbon upon completion of his Military Occupational Specialty training.
When going through the metal detector at the Pentagon, Mulder is talking on his cellphone. He sets off the detector the first time through, gives his keys to the guard, and makes it through the second time but is still talking on his phone.
When the limo drives past the gate to the base, a Canadian-spec speed limit sign is visible in the background "MAXIMUM 20", albeit with the "KM/H" whited-out.
General Bloch is wearing the belt of his service uniform upside down (the "male" side of the belt goes to the right, the "female" to the left - therefore the the end of the belt should point to the left of the wearer).
General Steffen's ribbon rack is out of regulation. At the very bottom left there's the South Vietnam Gallantry Cross, United Nations Service UN Korean Service Medal, and Republic of Vietnam Campaign Medal in respective order on his chest. However, the Gallantry Cross and Korean Service Medal should be flipped.
As the band begins to march, Scully and Skinner are running through the formation to get to the Jeep behind it; this is called "breaking ranks," and is considered one of the ultimate faux pas for bands and other musical corps. Marching bands have their roots in the military. Scully as the daughter of a Navy Captain and Skinner as a former Marine would both know this.