I suppose it can be argued that things may have happened differently for the character background in the S2 timeline, but I tend to work on the basis that it was largely the same as what we saw in S1, with the obvious exceptions of Claudia and moving to the ARC at an early stage. If you argue that Connor did a different degree, then how did any of them ever get involved, since it was Connor coming to Cutter and Stephen that sparked off the entire thing for the team. If Connor doesn't have that academic link with Cutter then the whole thing falls apart.

True, all of this can be explained away by 'sloppy writing', which is a real shame. I'd like to think that the writers did put more thought into it than that.