During the scene where Jack is practicing to re-qualify with his Beretta 92-F, he fires several rounds into his target. When we see him remove his target and show it to Mulder, the breech (slide) is closed. In the next scene with Jack turning around to put the target and gun down, the breech is open.
Scully mention the time to be stop at 6:47, where when watch is showed the time is 6:54.
While directing the search for Scully, Mulder says that "200 units of NPH insulin were taken, along with a box of syringes" from a drug store break-in. All vials of insulin sold at that time were sold in 10-milliliter, 1000-unit vials.
Even though Scully says the watch isn't working, the second hand can be seen moving.
While the doctors are working to revive Jack a ventilator can be heard on the soundtrack. There is no ventilator in use at any point.
When Willis/Dupre is re-qualifying at the shooting range his Beretta 92 experiences a stovepipe jam. Note the empty casing wedged between the breech and barrel chamber. FBI agents are trained to clear such malfunctions and continue firing. Dupre would not have known this.
Mulder says that the kidnappers were using a mobile and it can't be traced. Mobile calls were routinely traced by the police using contemporary (1994) means. Even the "signal check" broadcast gives a signal to triangulate and find the location of a mobile that is turned on.
Scully describes Jack's high sugar intake from soda causing him to suffer from high blood sugar. She describes high blood sugar as hypoglycemia, but he would be experiencing hyperglycemia. Hypoglycemia is low blood sugar.