A lot of her attempts at being adventurous end this way.
What exactly happened? Even I can’t answer that, however I would say that while Fluttershy is most likely very innocent regarding kinks and fetishes, she’s almost certainly well versed in the mechanics of procreation and that likely extends to the various animals she cares for. I guess there was likely an uncomfortable attempt at recreating rabbit mating rituals and possibly some role-playing that included a request for a litter and the like.
You can view this as a gif instead if reading this tall sucker is a little much: