well, if the issue continues, I’d recommend limitied their roaming spaces and adding more litterboxes until their box habits improve. Once they’ve mastered using the box in an area, you can slowly increase their roaming room.
Buns mostly don’t like to be held, think how it must feel to them as a prey animal – they’re up in the air and not having control over what’s going on.
Are your buns just unhappy about being held or are they really distressed and freaking out? Holding a struggling and kicking bun is not only dangerous for people (sharp claws!), but also for the rabbit since they can actually break their back.
If it’s just an issue of not liking it – to help bunnies feel more comfortable, pick them up every day or two, but not always with a grooming purpose. Just give them a hug, pets or a treat. this will help them to not expect doomsday everytime you pick them up. This will help them be less spooked about it, but it’s unlikely they’re going to decide they LIKE being held.