Possible reason for the ending (spoilers)
Maybe the whole thing was just an alternate reality / time shift test, just like how Max had said. If they can create another dimension (the hypercube) out of thin air, it wouldn't be an issue to create copies of humans to put into the cube. When Kate pops out on the other side, they most likely shot her to tie up "loose ends"... while her other body is safely wrapped somewhere in cellophane, unaware of the events that her "copy" went through.
Hence "phase 2 has been terminated".
I'd say it's open and shut, all things considered. She was only in there for just under 7 minutes, meanwhile Simon ages 10 years living off of endless Jerry clones. It'd be kinda funny if there was another guy in the cube named Ben.
Anyone that says this movie isn't plausible isn't a true science fiction fan, has too much time on their hands to write a 30 page essgay on it, and is nowhere near the realm of critical thinking.