I could see how a broken rib could have happened during a fight, as bunnies can fight by holding on to the other bunny with their teeth while they use their powerful back legs to kick their opponent. I would think fur would have been everywhere and the shelter would have then noticed that and did a check. Of course, if it was just a quick rough and tumble, the fur could have been minimal and just floated around and not noticed during clean up.
It's possible your other bunny had it and passed it on at some point. Jack remained negative for e.cuniculi even though his bonded mate was positive (never any symptoms though), so you just never know. 1 and 4 rabbits is to have e.cuniculi - however, most won't be symptomatic. Sometimes symptoms will show up only when the immune system is compromised. Stress can do that. But as far as "stress" goes, there is no blame for that. Bunnies, by nature, can be easily stressed and so it's just part of being a prey animal.
I guess there is really no way to know what's going on at this point but it's good that your vet is treating for for e.cuniculi just in case.
For now, I'd just hang out and pet your bunny. Since you can pick her up, just pet her -- bring over a book, laptop, phone whatever, and just give her as much attention as you think she craves and needs.
IF it is hind leg weakness due to e.cuniculi, there can be ways to help with balance and strengthening the best you can (as the real issue is the how the brain and legs are communicating). I had a bunny who had hind leg weakness as well and did improve.
For now though, concentrate on just following the vets instructions and keep her confined to help her rib heal. Give her toys and things that may help her pass the time if she is an energetic bunny normally.
Keep us updated.
Sending healing vibes!