How big is her space ? They need little space while they are litter training.

As Reeem said it may be due to the fact the area is too small that she might think the whole ‘area’ is her toilet. It may also be because she doesn’t feel like anything is ‘hers’ and she is trying to mark the territory. but usually this stops after a few weeks as the rabbit realizes no one is gonna take it from them. Do you have any other pets that might make her feel like her territory is threatened? a good trick i have found is that rabbits like to eat and poop. So i always put any hay i feed them in their litter tray. If i have just cleaned it i sometimes put pellets in their too. That way any time they want hay they have to go in the litter tray and it kinda ‘trains’ them to know that that’s where they eat and poop. It could be a number of different things. She might also just not like where they are and wants to tell you where her preferred peeing spot is. There is also the case that some rabbits just don’t always poop in their litter tray. Mine don’t. I have two that will pee every single time in their tray, and another who, if she deems it unclean will just pee next to it on the floor. All three of them leave the odd poop out for me when i get in from work. Good luck though and i hope you figure it out

Whats her bedding in the hutch ?