When Bo is shooting at Rawls in the house he is using a semi-automatic pistol to shoot Rawls. Bo runs out of bullets and you can hear the hammer clicking 3 or 4 time after the last bullet is fired. When a semiautomatic pistol runs out of bullets the hammer no longer works since it's the slide moving back with each round discharged that cocks the hammer. Being out of ammunition he would not have been able to click the trigger and have the hammer fall repeatedly. The gun would not have made any noise at all once it was out of ammo.
When Trevor and Scully were in the phone booth, why didn't Rawl's just use his hands to go thru the metal portions (corners and bi-fold of door) of the booth and pull the doors off?
Rawls is supposed to be unable to take his clothes with him when he passes through walls, but when he chases Scully and Trevor into the phone booth and is running around it, there is a brief glimpse of his boxers.
Just after Jackie Gurwitch gets off the telephone she hears a noise, and crouches down beside the kitchen counter. We see a crew member's shadow on the counter behind her.
When June runs Pinker down with the station wagon, he passes thru the hood and the engine of the car. They have been making a big point of how he changes the molecular structure of the things he passes thru, turns bullets to powder, Makes walls brittle enough to put your hand thru, makes steel brittle enough to be breakable by just bending it, then why doesn't the car engine explode when he goes thru it? It even stays running until Mulder turns off the key.