When Jesse begins the procedure on Lexa he says it's 3:26 AM. A minute passes and she "dies" - the computer announces the time of death as 4:02.
The small cube where Lexa was held didn't seem to have any... "facilities." That can create very uncomfortable situations...
We know from the past that Adam has Sanctuary rigged to thwart all of the Mutant X team's powers - it seems odd he'd forget to protect the floor, and in other episodes with defenses that thwarted Jesse's dematerialization either the floors were protected, or Jesse didn't bother to check them.
We've seen Jesse "drop" when dematerialized before (in first season's "Ex Marks the Spot"), and it was a slow "drifting" process. Here when Jesse goes through the Sanctuary floor, he drops at the normal speed of a falling body.
Gonsalves: You should be thanking me. When Eckhart first brought you to me, you were just an average operative. Under my control you were a virtuoso of violence.
Lexa: I disagree. (slugs him repeatedly) I was never average.
Shalimar: That's a big knife - compensating for something?
Shaliamr: Are we going to see you again?
Adam: If I'm lucky.
The Man: Mr. Kilmartin.
Jesse: Wha? Who? How did you...?
The Man: No time for eloquent questions.
Lexa: I think you just like to play doctor.
Jesse: You wish.
John Shea is listed as Special Guest Star.