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.
Plot hole: When Arthur wakes up on the bus, he sees an alien reflection in the window beside Josh, but it's not possible that the reflection could be seen at all - especially from the angle that Arthur first sees it - considering how much of the pillow is covering both Josh's face and the window. The pillow extends past Josh's face so he could lean on it as cushioning against the window, but somehow Arthur sees a full facial reflection.
Plot hole: After Exley has gotten up after being hit by the ball, Dales notices green alien blood inside the glove where the back of Exley's head was resting. However, Exley was hit in the face, not the back of the head; not only was there no bleeding face wound while he was on the ground, but the glove was clean when Exley first gets up.
Plot hole: When Arthur looks closely at the green alien blood on the baseball glove, he has no reaction to it, despite the continuous pattern in the show about the blood being incredibly toxic to humans, even from a distance. It should have badly hurt his eyes at the least.
Plot hole: It is virtually impossible that such a conspiracy-experienced, cautious, and wise person as the Second Elder would be so naive and careless to just let the "Dr. Openshaw" faceless alien to his house, knowing from the CSM that Dr. Openshaw had died that evening. (00:15:10)
Plot hole: Josh Exley's 'real' face shouldn't be visible as a reflection on the window. It's not an illusion that he creates to fool people, whereby his real self could theoretically be seen in a reflective surface, but a complete physical change, as we've seen in many episodes of the X-files regarding the shape-changing abilities of the aliens. What his face appears to be while altered is essentially what it is, and the reflection should show as much.
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.
