I don't think it's a chemistry issue. Paul Carter transferred to be closer to his sister, who is battling cancer and faces some serious surgeries in the near future. You just don't question the motives there, as it seems like a very legit reason. I've seen someone write something about how Paul's dad had indicated that it was more than than just wanting to be closer to family, but he didn't go into detail. The fact is that the major reason behind Paul's transfer was family-related.
As far as Cobbs, my guess is that it's two things: a potential lack of playing time, and the weather/distance from home. If he ends up transferring someplace that's just as far from home, then you can question that second motive, but the playing time thing would seem to be the reason, not a lack of chemistry on the team. If/when Al Nolen returns, Justin was looking at the probability of being the third or fourth option at point guard. Nolen, Devoe, and Cory (if he signs) would all rank ahead of him.
So, let's not make more of this than what it is. The new talent coming in is just going to continue to make the Gophers stronger.