Plot hole: Agent Spender watches in horror as Alex Krycek stabs the neck of an alien directly in front of him and the usual bubbling green blood spills out. In every other instance of a human being in such close proximity to the green blood, the person has immediately taken a painful reaction to the substance, including severe damage to the eyes. Spender however is completely unaffected, as is Krycek, who was also close enough to feel the effects.
Suggested correction: The Syndicate is well aware of the effects that the alien blood has on humans and the inherent risk of being exposed to it. They would have inoculated Spender and Krycek in preparation for this.
There was no inoculation ever mentioned to counter the effect of the acidic blood. Also, Spender wouldn't have let someone randomly inject him with something with no explanation, it would be completely out of character, and he was surprised at what happened.
Suggested correction: I think that this is to do with where he is hit. I don't recall anyone suffering the toxic effects when the weak spot at the back of the neck is successfully hit with the spike weapon. When Mulder tried to kill the alien bounty hunter (think it was in Colony?) He missed the weak spot, which is why the blood had an effect on him and the bounty hunter survived.
Continuity mistake: When Scully walks into Mulder's office, she stops in the position with the "I want to believe" poster in the background, then she takes a couple of steps to make acquaintance with Mulder, and she finds herself again in the position with the poster in the background. (00:05:15)
Trivia: Rebecca Toolan plays David Duchovny's mother in the series, even though in real life she's only a year older than him.
Suggested correction: This entry is actually incorrect. There are records that prove she is much older than what's stated. By 1968, she married her first husband and was a university professor. Https://www.newspapers.com/clip/22109182/wedding-announcement-rebecca-cox-and/.
While there are many conflicting reports about Rebecca Toolan's age, it seems the Wikipedia entry is the most incorrect (which is where you got your source). It seems more probable than not that whoever edited her Wikipedia page linked a article about the wrong Rebecca Toolan.
Factual error: When two unidentified men who approached Susanne Modeski in the warehouse take out their handguns, they have regular pistols. However, when they start to shoot, continuous fire is heard that could only be produced by an automatic weapon. (00:28:40)
Suggested correction: Fully automatic pistols exist, such as the Glock 18.
Plot hole: Big Mike was attacked by the creature, because his bulb was broken just for a couple of seconds. It would mean that even if something like this happened to somebody else by accident, this person would also be killed by the creature. That would drastically increase the kill rate in the community. (00:16:15)
Suggested correction: That was the whole point of the creature, to enforce the HOA rules so that no violations occurred, even by accident. Although prior to the attack, Gene Gogolak describes Big Mike as a weak link that had to be dealt with, so the bulb was just an excuse to attack him.
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.
