Were there any other females bettas in the tank? When my 3 girls were together, Reena would chase the other girls till they did exactly that, stay at the bottom or behind something, not move, hiding.
An aggresive alpha female may be trying to assert herself in the tank. There is not much you can do other than seperate them. Once you remove a female from a community tank, very often they cannot be reintroduced because the other females will gang-up and attack her.
A lot of breeders experience this when using a female from a community tank and breeding her to a male. Once she leaves the tank, the community will often not take her back.