In the beginning of the show, the doctor is talking to the patient and saying how he'd tried to kill himself three times in the past three days. When the doctor walked out, the patient got up and went to the hydrotherapy room where he tried to kill himself for a fourth time, unsuccessfully. In real life, a suicidal patient would not have been left alone and unrestrained, especially immediately after attempting suicide three prior times.
Both the hospital administrator (general) and his female adjutant are shown wearing infantry officer branch insignia (crossed rifles). Hospital staff would be medical or medical service branch. Also, at the time the story takes place, a female soldier would not be allowed in the infantry branch. Shoulder insignia on general is incorrectly placed (too low).
Captain Draper's ribbons are in the wrong order.
Captain Draper is missing the National Defense Service Medal on her uniform, which as a Gulf War veteran, she would have. She is also missing the Kuwait Liberation Medal and Army Service Ribbon.
The colonel rank insignia on the doctor's lab coat lapel at the start is the large size one worn on shoulders the ones worn on collars are much smaller.
Rosslyn is misspelled on Victor Stans' patient record. It is spelled with two Ss.
Stans' service record at the start is clearly for a Marine, listing USMC commands and terminology. However, Stans was an Army officer.
Captain Draper's uniform is missing the National Defense Service Medal ribbon, which nearly every soldier in 1995 would have.
General Callahan refers to Captain Draper as his Adjutant. The Adjutant of a Two-Star General's Staff would be a Lieutenant Colonel. Captain Draper is General Callahan's Aide.
Captain Draper tells Mulder and Scully that "military protocol" requires that any criminal investigation of military personnel be conducted by military criminal investigators. This is actually a requirement of United States Federal Law and the Uniform Code of Military Justice. "Military Protocol" is a set of guidelines for social functions (such as which flags should be displayed, and the correct order to display them), and is frequently confused by writers with customs and courtesies observed by military service members and military law.
After General Callahan orders Captain Draper to get some rest, she salutes him and leaves. Contrary to popular myth, the U.S. Army does occasionally salute indoors (when reporting to a superior officer, at the end of a staff meeting, etc), however saluting on this occasion, while not technically incorrect, is not actually called for and could be interpreted as insubordinate.
While searching for Lt. Col. Victor Stans, Scully yells out, "Lieutenant Colonel." A Lieutenant Colonel is always addressed verbally as "Colonel" as a military courtesy, except in writing. An FBI agent who has frequent contact with the military would be familiar with military customs and courtesies.
At 42:15 as Mulder approaches the fallen two-star general in the hydrotherapy room, he calls him "Lieutenant Callahan."