Yes, it happens sometimes. It's more frequent with same sex couples, but it can happen with male / female too. To begin with, some bunnies hate rabbits. I've known a doe who couldn't stand to share her space (I remember the woman who had her saying that she binkied like crazy on the day her two other rabbits were at the vet for their spay / neuter and kicked up a storm when they came back home) and tried to gut every rabbit she met.
There are also rabbits who just can't stand each other. Aki hated Tybalt when she met him - he is dirty and lazy and can't be arsed to follow the correct rabbit etiquette whereas she's a complete neat-freak and very dominant. They got over it, eventually, but I really thought it wouldn't work.
Sometimes, you need to persevere. I'm pretty sure there is an article on the house rabbit society website about a couple that took several YEARS to bond. It worked in the end, but it was very difficult (I admit, I would have given up much sooner).