So. Possibilities.

1) Weapon X and the Shop are two branches of the same seekrit gubbmint organization, tactical and research, respecitvely.
2) Weapon X and the Shop are competitors
3) Weapon X and the Shop don't know about each other (yet).

I feel that 3 doesn't make sense, if both are kidnapping mutants of reasonable power level. It's not a huge population. For purposes of plot, 2 would be a clear reason for Kurt come in a tactical strike sort of way, but 1 has its own interesting plot options.

Assuming 1, here are some options:

1a) Okay okay, we should teach the German kid English 'cause he'd be more useful, but we don't want to bother TEACHING him so get a telepath to do it.
1b) Kurt is burned out beyond the point of usefulness. Repair our weapon, pls.
1c) The Shop has some project they're going after that warrants Kurt being reassigned there to help.

Assuming 2,

2a) The Shop and Weapon X are both trying to collect the same target, and their field operatives have a run-in.
2b) Weapon X wants someone from the Shop for their own (Gabe or Allen?) and sends Kurt in for a grand yoink.
2c) Weapon X has decided to take the Shop out and has sent Kurt in for a tactical assassination.

Thoughts?