Scully's bandage has a spot of blood when she gets out of the car to talk to Mulder at 14:44 and clear tape just above the bottom of the gauze with some gauze sticking out from below it, she is also wearing the bloody sweatshirt that she had on the night before, but when she calls Mulder the bandage and her clothes are different at 18:51.
4:44 - The glass top of the table breaks 3 frames before she hits it. Under the table there is a black box at the top of the left leg just under the glass, with a wire connected to it, that runs along the inside ledge of the table. Just before the glass breaks there is a flash from the box. And later when Scully sees the table, the box and wire are gone.
4:25 The Bounty Hunter threw Scully against the wall, several feet from the chair. Yet at 4:44 it is obvious that when he throws her to the table she jumped from the chair.
After Samantha's body is pulled from the river, the body is loaded into an ambulance that carries the letters "FBI." The real FBI doesn't operate any ambulances.
The flag in Skinner's office is hung upside-down.
Scully: Did you find what you were looking for?
Mulder: No... No. But I found something I thought I'd lost. Faith to keep looking.
X: You'll only win the war if you pick the right battles, Agent Mulder. This is a battle you can't win.
Skinner: What's going on here, Agent Mulder? Why are the lights out?
Mulder: Orders from my opthamologist.
Bounty Hunter: Is the answer to your question worth dying for? Is that what you want?
Mulder: Where is she? Just tell me where she is.
Bounty Hunter: She's alive. Can you die now?
X: You wanted to see me?
Mulder: How was the opera?
X: Wonderful. I've never slept better. I don't like these hasty public meetings, Agent Mulder.
Mulder: I'm sorry. I need your help.
X: It's over. The fat lady is singing.
In order to recreate the Arctic, a large soundstage had to be filled with 140 tons of ice for 5 days.
In the original script, Samantha would have survived the fall off the bridge. Once she had been rescued from the river, she would have driven with Mulder to the clinic. However, once they got there, she would have transformed into the alien bounty hunter.
The first takes of the fight between Skinner and X were rather weak as both actors were too preoccupied with not hurting the other. However, after a few takes, the director asked them to heat things up and both decided to just go for it. In the next take, the fight became so real that Mitch Pileggi threw Steven Williams against the (fake) elevator wall so hard that he went right through the back of the set piece.