This is my experience:
When Mocha ripped Fey's stomach open, the emergency vet stitched her up and gave us four days worth of Meloxicam (pain reliever/anti-inflammatory) to be given once a day and a week worth of Baytril (very common antibiotic) to be given twice a day. Fey was okay with her meds at first, but soon developed problems with the Meloxicam. After her daily dose, she would not poop and would hardly touch her food for 10-12 hours. I stopped that early. My regular vet said that this side effect is not unusual, which is why he usually only treats pain in rabbits for the first day or two and then withholds painkillers unless the rabbit does much better on them. I had mainly heard of the need for continued pain treatment in rabbits, not the severe side effects that painkillers can cause in them.
The Baytril was okay for longer, but Fey started to get slightly mushy poops before she had her last dose (last Thursday). It got worse over the weekend. She started having occasional mucous-covered poops and some liquid feces. I removed all veggies and treats (except for a little oats). My vet said that there's not a whole lot to be done, but advised to feed her small amounts of dark leafy greens. He did not want to give a probiotic because she reacted badly to her previous meds. She was back to normal in a few days, and I was able to feed her veggies like normal again.