I don't know exactly what happened to Jones, but one thing I remembered is that Jones originally died by getting sliced in half by Peter Bishop. And Jones essentially turned to ash on the same side that Peter sliced off. So maybe there's some correlation there? As to why he turned to ash I have no idea... or even why the beatdown he received was enough to kill him. Color me confused too.
Overall I was a little underwhelmed with this particular episode. Yeah it was cool to see Bell back but if this were the 2nd to the last episode ever, I would have been severely disappointed. Let's hope the season finale brings it all together (Bell, Jones, the universes, the Observers, etc.). Although I really don't see how it could.