I’d take it back a few notches. That is terrible advice to just let her out of her cage at the same time. Bonding needs to be slow and patient. The vet really wanted you to rush things. Did you do any prebonding? Switching them between their enclosures or switching items between their enclosures? Bonding sessions should start at 10 minutes for a few days or even multiple times a day, and then gradually increase the time in 10 minute increments leading to 60 minutes, then you can start increasing by 30-60 minute increments. I’d go back a few steps and prebond (if you didn’t initially), and do that for another few weeks. She’s still new to the environment, and three weeks isn’t really a lot of time for her to feel comfortable and adjusted yet, especially with a bunny trying to constantly mount her. Go back to prebonding, give her a little time first before starting this, and then after a month of successful prebonding (you shouldn’t see any aggression when they’ve switched spaces), then you can start with short 10 minute sessions, and gradually move up to longer sessions when no incidences have occurred for at least 3 play dates.

I just noticed she isn’t spayed. Bonding them isn’t going to be easy as bonding should be between two fixed bunnies. He’s likely going to continue to feed off of her hormones and act hormonal. So the humping, in theory, may never stop. She could also turn and become aggressive to him, again, due to the hormones present.

I hope your poor girl is doing better now

There have been people on here who have bonded an unspayed female with a neutered male, I think that’s easier than the other way around. Good luck When you start bonding, it might be helpful to keep a bonding journal just to track everything.