Plot hole: In Ben's nightmare, Gwen says, "We will come and get you!" and then she nags at Ben for being the one with the alien powers, and she does not join him in climbing the tree. My guess is that this was due to a script error; it was likely supposed to be "he" (i.e. Ben) instead of "we".
Back With a Vengeance - S2-E13
Plot hole: It is rather strange that grandpa Max would have a kid-sized Plumber suit ready for Gwen, given a) that the Plumbers are effectively defunct, and b) that a government organization would hardly allow underage trainees in their ranks.