I've rationalized it before by saying that maybe Zach paralyzed Bobby, because he threatened to do so before Castiel showed up - and Castiel told him to "put these boys back together" but didn't say anything about Bobby.
But the other thing that just occurred to me is that Bobby was possessed! We still don't know how Bobby CAME to be possessed. We don't know what happened between Bobby being possessed and Bobby showing up with the Impala. And what was one of the very many lessons on demon possession learned in Devil's Trap back in S1?:
Demons can heal a body AS LONG AS THEY ARE IN IT. As soon as Dean got 'Meg' out of Meg Masters, Meg Masters died, because she had been thrown from a window and shot. Once the demon is no longer in the body, all injuries incurred return...and while a demon is in a body, injuries have no effect. Bobby shot Ruby with a defunct Colt and all it did was ruin her shirt - she was still walking around the rest of the season with a bullet in her heart. The guy in the Hunter-couple we met in the Magnificent Seven drank draino - which would have destroyed his vocal chords (along with killing him) but a demon was able to yell for the guys wife using the dude's body an hour or so later.
Basically, what I'm saying is that, Bobby's lower spine could very well have been irreparably damaged BEFORE he stabbed himself - it could have happened in whatever scuffle there was when the demon attempted to possess him.