Buns don’t like to be picked up or held, she is showing discomfort by hiding and thumping. Rabbits are not normally noisy, so the fact she is not vocally protesting is not a sign that she’s okay with this.

For example, it would be less troublesome for her if she was moved around in her carrier.

Rabbit’s can’t whine, so it’s not unusual that she isn’t making noise to express her dislike.

You say she’s a couple of months old, and rabbits tend to be super friendly and calm as babies, but get more resistant to being held the older they are, so it’s probably to do with her getting older.

There is no such a thing as a play thump. They stomp out of anger or fear. For example, I put my bunny in the carrier to take her to the vet on Saturday, and she gave a loud stomp of anger.

Bunnies generally don’t like being picked up or being off the ground. So she’s thumping to let you know she is not happy. My bunnies have never stomped for play – they do stomp if something startles/scares them or annoys them. Peanut has been known to stomp if I’m not quick enough topping up his hay too  and he stomped at my boyfriend yesterday because he walked past him in his boxers 

Thank you for spending time with this bun! You interacting with her is probably the best thing in her life, and she shows that by licking your face and pushing her head into your hand for more pets.

As for not liking to be picked up, that’s perfectly normal for a bun. They can tolerate it well as babies, but as they mature their instincts kick in and “tell” them getting picked up means you’re about to become somebody’s dinner. So they try to avoid it. Some buns can get quite defensive and lunge and box and growl if you corner them. Buns don’t whine, but if they are terrified they can let out really blood-freezing cries. I hope you’ll never have to hear that from any bun, but it’s good to know that it can happen.

Play thumps do exist, but it’s rather unmistakable when thumping is about the bun being overcome with overwhelming lust for life. It binkies and make series of short runs with 180 degree turns, it can throw in a thump here and there for good measure. It’s like it’s showing off all of its repertoire, and that might in a way be what it’s about: A young bun displaying it’s excellent health and good vigour. It’s attractive to prospective mates and it can also deter predators, because predators look for weak prey. From what you describe about the situation, I rather  think “your” bun is thumping to inform you that she’s displeased.

Sarah, that’s just hilarous, Peanut stomping at your bf in boxers =D =D =D

It sounds like she’s started puberty. Not as playful, more skittish, plus she poop marks. Bunnies poop mark their territory, so it’s normal but it is of course inconvenient. You can try with an additional box, but marking is an instinct and it will be at its worst while she’s a teenager with raging hormones.

I think buns can handle the necessary evil of being carried inside and out. It rather depends on the bunny, some are more fearful and won’t get used to being carried. Picking a bun up often to desensitize it to being picked up can either make things worse, or better. You’ll have to judge by her reactions.

Some buns do like to snuggle in a human’s lap. My bun Bam does, but it’s taken us a long time to get there. It always has to be his choice though – if he isn’t in the mood for cuddling he’ll nip my arm as a way of telling me to put him back down on the floor.