Via Negativa - S8-E7
Revealing mistake: When Doggett examines in the car the body of Agent James Leeds, the carotid artery of the victim is pulsating. (00:05:40)
Via Negativa - S8-E7
Continuity mistake: At The Beginning of the scene, there is only what seems to be a remote control on the left-hand side of the TV. Five seconds later, a couple of VHS tape cases appear where the remote control was before. (00:08:46)
Via Negativa - S8-E7
Continuity mistake: When Doggett and Skinner visit Dr. Andre Bormanis at his place, in the first shot from the back he is leaning over some laboratory gear that is holding in his hands, while in the next front shot he is standing upright manipulating on the table with his hands. (00:18:10)
Via Negativa - S8-E7
Continuity mistake: When Doggett leaves his office, he reaches for his coat, grabs it and starts to put it on. In the next shot, when Langly, Frohike, and Byers look in Doggett's direction, we again see that he takes the coat off from the chair. (00:27:55)
Continuity mistake: In the opening scene, when the guy is calling from the booth, he is standing either on the left or right side of it, depending on the shot. (00:00:40)
Continuity mistake: Randall has strange pale eyes but just before he shoots Dwight, when he is aiming the gun at Tammi, there are several close ups of his face and his eyes are a normal brown.
Other mistake: Larina dials 4, 1, and 4, but the voice in the phone says, "This is operator 525." (00:23:25)
Continuity mistake: When Ray is eating the sandwich, there is a large bite out of one corner just before he removes the foil. In the shot from behind after the foil is removed, the bite is only from one slice of the bread.
Continuity mistake: Just before he removes it, the foil disappears from Ray's sandwich in one shot, then appears again in the next shot.
Factual error: Dogget says that "It would require something 4,300 times the density of steel to cause this damage." Steel is about 8 times denser than human flesh, so bearing in mind that density is proportional to mass at constant volume, it means that Ray would be 4,300 x 8 = 34,400 times heavier than if he were a regular human being. Assuming that he normally weighed about 80 kg, after the transformation he would weigh 80 kg x 34,400 = 2,752 tons. It means that hardly any ground would support his incredibly huge mass, let alone items such as a bed, chair, stairs, building structures, etc.
Revealing mistake: The establishing shot of Boston General Hospital at The End of the episode shows the same porte-cochère that was used for the BYU Medical Center in Provo, Utah eight episodes earlier in "Roadrunners." It appears they just digitally inserted this portion of the building over different facades. (00:40:00)
Suggested correction: These are two different porticos. The columns in the Boston picture show concentric grooves, and the fascia on the front of the roof structure is smooth and rounded. The Provo portico has smooth columns and the front fascia is composed of flat rectangular panels. In both pictures the porticos seem to be well-matched to the building structure and landscaping. It's unlikely that the production would have gone to the considerable expense (in the 1990's!) of a digital enhancement.
I could have worded the entry better, but while it's not the exact same portico, it appears to be the same building, but different entrances. The two structures have the exact same kind of writing on the right side and the overall design of the structures is remarkably similar, with some subtle differences in the columns and fascia, as you pointed out. Seems highly Improbable that a building in Boston and another in Utah that are not supposed to be affiliated with each other would look so alike.
It's also worth pointing out that the shot of the BYU Medical Center from Roadrunners showed the Kansas state flag flying outside the building, suggesting that the crew either had stock footage of the building, or they happened to be in Kansas and filmed the building in question. It's highly unlikely they went to the effort to find stock footage or actually went to a different building with a similar looking portico for the sole purpose of using it as an establishing shot of a different hospital in another episode.
After studying the photos again, I would have to agree that it is probably the same building, probably with an addition added to closely match the original construction. As to the improbability of two hospital architectures being so similar, I would reply that this may be common. I had occasion in the 90s to visit a hospital in East Lansing Michigan and later one in Alexandria Virginia that were virtually identical and owned by different health care systems.
Continuity mistake: When Scully enters her apartment, the blinds are up and there is quite a lot of light in the room. However, when the flashback with Mulder ends, during which Scully was supposedly standing still, the shades are rolled down and there is much less light in the room. (00:20:30)
Three Words - S8-E16
Continuity mistake: When Mulder sits at the computer terminal in the census records room, we see two empty boxes on the screen, one for an ID and one for a password. The shot cuts to Mulder, then back to the screen and shows him typing the password, while the ID has already been typed in; it is very long and there wasn't time in between shots or nearly enough clicks of keys for Mulder to have entered that ID.
Empedocles - S8-E17
Continuity mistake: When the fiery figure comes up to Jeb, he is standing alone on the street, however in the previous and following take he stands in the crowd surrounded by other people. (00:02:15)
Continuity mistake: When Knowle Rohrer is talking with Agent Doggett face to face in a separate room about the super-soldier project, he is wearing a red FBI badge, but in the previous scene when he came to visit Doggett, he was wearing a regular FBI badge. (00:08:40)
Continuity mistake: When Agent Reyes and Agent Scully are talking about mood music, in some shots Reyes rests her hand on the bed's backrest, while in other shots she firmly grabs it. (00:14:45)
Continuity mistake: When Agent Reyes is aiming at the oncoming car of a ranger, in the front shot the windscreen of the car is completely covered with dirt and fully opaque, while filmed from the ranger's side the windscreen seems to be transparent and relatively clean. (00:17:00)
Continuity mistake: Just before Skinner shoots Alex Krycek in the head, Alex is lying weakly on the ground, having already been shot twice. However, as Skinner makes the kill shot, Alex is suddenly standing and falls to the ground upon impact of the bullet, with no time (or strength) for him to have risen. Also, the last shot of the dead Alex shows his face and his nostrils flare from breathing.
Nothing Important Happened Today (1) - S9-E1
Character mistake: When Agent Dogget is eating breakfast, he listens to the information in TV news about "the body of 38-year-old Carl Wormus." However, the obituary which Agent Reyes is reading later says that "Carl Wormus was found dead at the age of 45." (00:07:30)
Nothing Important Happened Today (1) - S9-E1
Continuity mistake: During the previous episode, Skinner receives a nasty gash on his head courtesy of Billy Miles. This episode takes place 48 hours later and there is no indication whatsoever that Skinner received such an injury (the wound is visible once again in the next episode). (00:15:35)
