I think it was because the prison was overrun with walkers shortly thereafter. They're everywhere by the time Michonne comes back, & not only had they spent much of their ammo & been split up, the fence had been run down by The Gov's army (Which was a pretty stupid strategy, come to think of it) WTF were they going to do with a fenceless prison?In fact, why did they run off in the wild blue yonder when it was not necessary? The Governor's small group was largely dead by the time Daryl destroyed the tank, so they did not have to run far.![]()
The same thing they did when first finding / securing the prison--which had a partially destroyed fence, a giant hole in one of the walls, and walkers in the yard, not to mention the halls of the prison. Or, the same thing when inmate Andrew flooded the yard/halls with walkers. The other advantage was an increase in firepower, which was effective against the massive herd faced by Rick & Carl.
Ultimately, they were in the prison, and modified it to suit their defensive needs after (what is assumed to be) more than a year inside, so it is impossible to think they would have positions set up in case of a walker invasion?
I didn't mind that Michonne managed to walk among the zombies so much. I mean, it was a bit of a stretch, & they could have minimized that a bit had they covered her up in some guts like Rick & Glen in S1, but still, I'll get over that too. I clump that one in with the mystery of what zombies can & can't do. They get a little bit of slack where the sci-fi angle comes in, imho
Even in sci-fi/horror/fantasy, certain established rules matter, or there's no consistency. Michonne could walk in the middle of a pack undetected, yet Andrea had to kill a walker near the prison entrance, despite the use of another as "camouflage."