When Scully is typing the report in her apartment, her computer screen goes from white text on a blue background in the extreme closeup to white text on a green background in the medium shot and back to white on blue again in the wide shot.
When agents Scully and Purdue are viewing the archived footage of the warehouse standoff, it is all a single wide shot, presumably from a security camera. At the end of the scene's dialog the camera pans back to the TV monitor, where the tape is on a freeze frame, but the shot has tightened up to a medium shot focusing on the relevant plot detail.
At 10:35 Mulder gets into his car. Comparing the close up to the wide shot seconds later, the distance between the parked cars changes.
(at around 43 mins) Young Barnett is seen in the hospital with a bullet wound on his left shoulder, received from the shot fired at him by Mulder. However, his left shoulder was earlier hidden behind his hostage, so could not have been the target of Mulder's shot. Only his right shoulder was visible, which could have been the target of the only shot fired at him by Mulder. However, a shot fired at his shoulder could not have incapacitated him the way it was depicted, which could only have been possible with a shot aimed at his head. But, as seen in the hospital, his head was completely injury-free. Moreover, a shot fired at his shoulder should have also given his arm a strong backward thrust, which was not seen.
Around 00:43:12, you can see a ball socket falling off from Scully's Kevlar onto his hair.
The establishing shot of the recital hall, supposedly in the DC area, is actually the Carnegie Museum of Art in Pittsburgh, PA.
The judge orders Mulder from the witness stand without allowing Barnett's lawyer to cross-examine him, a violation of Barnett's rights under the Sixth Amendment.