It is wonderful they are free-roam and have such a good amount of freedom/integration. I think limiting them to a room or smaller segment over the weekend, when you can monitor them, is wise though.

How are their relationship with each other? Once they were neutered, did you go through any bonding processes? Perhaps there’s some bullying or dominance issues, which is translating over to actual house territory (reluctance to go to/leave specific areas). It’s only a potential, but maybe Pippin is bullying, thus he only is interested in stealing brussel sprouts when he see’s it’s being offered to Merry. Merry may be more friendly because he is searching for comfort in humans, while Pippin is on guard due to his relationship dynamic with Merry. He may be squeamish around you and your husband because you are both so freely navigating what he has established with Merry as ‘his’ territory.

… Those are just my quabbles of what rabbits may be thinking. Anything like this seem like a possibility?