My bunny moans loudly and thumps at night!?

We have had rabbits for many years, but have never heard one moan. They do thump to alert everyone that something is not right or that they are angry. She may not realize that she is not in danger as rabbits are prey animals. You may need to consult the "House Rabbit Handbook" to see what the moaning means. Spaying her will help unless you want to breed rabbits. That may stop some of the aggression.