Around 00:33:41, Mulder is holding the alien's special weapon in his right hand. On the next shot, the alien bounty hunter is taking it on the ground, far away from Mulder's hand.
Around 00:33:31, Mulder is holding the shirt of the alien bounty hunter with his hands. Around 00:33:38, Mulder is holding the alien's special weapon in his right hand.
When Mulder enters the hospital at 34:58, disheveled with no sidearm. When Sculley rushes to his side at 35:04, his sidearm miraculously appears at his side.
Around 00:32:56, Mulder is holding the phone along his body. On the next shot, he's holding the phone on his ear.
Around 00:33:41, when Mulder is on the ground, we can see padding under his trousers.
Around 00:33:40, we can see Mulder's stunt lining.
On the Telus work order, the head office address in downtown Calgary (10 Ave SW) is not actually for Telus, but a parking lot. The actual Calgary office of Telus is a few blocks away on 4 Avenue SE. The actual head office for Telus is ironically in BC, in the same area where the show was initially filmed.
Scully mentions that she has a unique protein in her biopsy as determined by "confocal microscopy" and "immunohistochemical staining" with an antibody. These techniques will identify the sub-cellular location of a protein, as long as the antibody is specific for it. However Scully then claims that this proves that she has a uniquely tagged protein. It does not - all it proves that the antibody has bound the protein that it is specific for, in this case cowpox structural protein number six. It could not show that the protein had a unique sequence added to it. Mass Spectrometry, possibly in conjunction with a Western Blot, would be needed to clearly show that she had a uniquely tagged form of the cowpox protein.