Continuity mistake: The establishing shot of the Agency's headquarters building zooms in on 3 tall, narrow windows recessed into a brick wall. We then cut to an interior view - of several wide, continuous windows without any recesses. They don't match the exterior windows at all. (00:07:30)
Continuity mistake: The assassin rips out a magazine page with Leila's photo on it and sets it ablaze with a cigarette lighter. The face in the picture burns while he's still holding the page. But in the next shot, after he drops it, the face is still intact and starts to burn all over again. (00:22:30)
Continuity mistake: When Darien reaches into the glass spider enclosure to retrieve the note, the number of spiders sitting on the paper changes (too quickly for them to have crawled away and back naturally). First there are two on top of the paper, then only one, then instantly two again. (01:11:30)
Factual error: Darien sets up a tripod and videotapes himself leaving a message for the Agency. When the tape is played back later, the camera can be seen to have both zoomed in and panned to follow his movements, even though no one was there to make those adjustments. (00:30:30)
Continuity mistake: Early in the first season it was established that Darien's parents died in an accident, and that he and his brother were raised by an aunt and uncle. But here, Darien's father is alive, is said to have "disappeared" years before, and there's no mention of the accident he "died" in.
Plot hole: In the pilot, it is established that the surface of anything/anyone made invisible by "quicksilver" is freezing. (Darien gets caught in the women's shower because the mist freezes on him. He freezes the beer mugs for the doctors.) But in later episodes, nobody notices him standing invisible - and freezing!? - next to them.