Fleas could have been transferred via you or your boyfriend, or they could have been around the outside of your house from wild animals, stray cats, etc. and made they’re own way inside. If your boyfriends cat has fleas and is inside, then his house will also have fleas. So while they don’t commonly attack people, he could definitely be bringing them over in his clothes, etc.
The vet was probably not specifically looking for fleas in an indoor rabbit, and they are hard to see unless it’s a pretty bad infestation. It’s also possible that the fleas have moved in, since the vet visit.
If it is fleas and they are fairly new, then Rupert wouldn’t be scratching too much because it hasn’t been long enough/bad enough to make him REALLY irritated.
I recommend giving your vet a call. They will either tell you to come in and they will try and pull a flea from Rupert and look at it under a microscope, or they may be able to prescribe you a RABBIT SAFE flea treatment over the phone. They may even recommend doing preventative treatment, if your boyfriend is having flea problems with his cat.