I've done a lot of reading on bunny behavior and it is not unusual for females to fight. They argue over food, space, the boys and especially who is going to be boss. In the wild bunnies live in a hierarchical society and they determine among themselves who is allowed to do what and where they can do it. This carries over to domestic rabbits as well. We think of bunnies, especially females, as cute and loving animals (which of course they are) but it is also in their nature to be territorial and become jealous of other buns. They may or may never work out their differences, some do and some don't. We have had to do a lot of separating of our bunnies when things don't work out at the sanctuary. Since Ebony is so small right now you have done the right thing by separating her from her sister for now. Perhaps later on when she is larger and stronger you might try to put them together again. So really, the sister isn't really being mean, she's just really being a bunny.
Good luck!