Not exactly a nitpick, but there seems to be some blurring between Moleculars and Psions. As in "Altered Ego," Henry is called a Psion, but uses a "toxin" to establish contact with his targets. Compare that to Emma, who seems to be a "pure" Psion.
Why doesn't Jesse at least initially do a phased sweep through Henry's subway car? Even if he can't sustain it for more than 30 seconds, a couple of passes would seem to let him figure out if Henry was there or not.
Laser beams aren't visible (except if the air is filled with smoke or heavy particles), and having a visible security laser web seems to defeat the purpose of having such a thing in the first place.
What's the limit on Jessie's ability to phase other objects with him? He needs to toss the lightweight key card because he can't take it with him (apparently - he might just be showing off but this seems unlikely given the dangerous situation). And he says he can't phase the Faberge Egg. However, he can phase his clothing and the radio headset with him. Are they specially treated perhaps?
As predicted, Eckhart's memory (wiped in the previous episode, "Presumed Guilty") is totally intact here, to the point that he remembers his favorite composer. That means that he knows where Sanctuary is, which clearly isn't the case in this and subsequent episodes.
Not exactly a goof, but what type of New Mutant is Zack? He can sort of project his consciousness of what he sees (a Psion), but has a kind of X-ray vision (an Elemental, perhaps) and his abilities certainly "defy physical science" (a Molecular, to quote the Genomex website). This point is never really clarified.
For some reason, Eckhart didn't leave any written or electronic notes about the location of Sanctuary given to him by Mark before going there himself, despite his typical paranoia.
Lena's second eyelid protects her from Mark's powers, but shouldn't sunglasses protect someone? Many GSA agents wear sunglasses - why did four of them have problems with Mark?
Megan's right hand seems to be hanging up in the air despite the fact she is laying on her back and dead. After Adam wakes up it is lying much more naturally.
Why didn't Adam know Mark's power? Wasn't Mark in the files they stole back in the first episode and that they've referenced from time to time since? And if he does know what Mark's powers are, why does he put himself in a position to be taken so easily?
Why does Eckhart need a mutant to take out Mark? Once again it seems odd that nobody bothers to use guns, or at least tranquilizer darts, and take out someone at a distance.
So Mark now has all of Eckhart's memories. Wouldn't that be invaluable to Mutant X and the Underground?
So why can't Mark access Adam's memories earlier, but has no trouble later when he leads Eckhart to Sanctuary? This delay seems to exist for no reason other than to pad out the story.
Shalimar seems reluctant to consider the idea that Adam is a murderer - why? He essentially order Caleb's death in "Lazarus Syndrome" (although Brennan carried it out). There were other ways to deal with Caleb (see "Trivia" for that episode) and Adam went with murder. So why is Shalimar skeptical, particularly if Adam might have some good reason?
Why can the virtual simulator still be used as a "virtual prison"? After Adam turned against the group in "Altered Ego" and imprisoned them, you'd think they'd put some kind of protocol in so the individual Mutant X members can override it and get out.
Would a prisoner being held on suspicion of murder really be put in a prison (as Lena calls it) immediately after they were arrested, as Adam is here? Typically you use a holding cell in a local precinct house until an initial hearing is held, motion for bail is put forth, a trial date is set, etc.
Unless the girls were shopping for weights on that trip to the mall, there's no reason why hitting the GSA agents with their shopping bags should have been any more than an annoyance. Maybe they just bought a lot of socks at Banana Republics. not socks. Those shoes Shalamar bought for 60% off must have been really heavy!
Jesse asks why the GSA are suddenly so successful at exposing their safehouses. This wouldn't happen to be the same safehouse they tracked his dad down to in "Blood Ties," is it? Seems like that one's fairly easily explained, at least.
When Shalimar is laying Emma's body on the bench in the club, you can clearly see Lauren Lee Smith open her eyes, lift her head up and place her hand on Victoria Pratt's back to help out.
For a group that's committed to not killing its opponents (something John Shea notes in his interview with SciFi Channel: "You notice in the violence that we do, it's a very stylized kind of violence in that nobody dies."), Brennan seems particularly ruthless in electrocuting Caleb. Again, why couldn't they knock him unconscious and imprison him? (also see above) And if you are going to kill people that go around murdering New Mutants, why not start with Eckhart? Killing Caleb in this episode seems like a very big mischaracterization of the team for the sake of a convenient ending.