As long as there is no fighting or serious aggression I would just leave them to it. Our girl is a bit like this with her bonded partner and is a bit sneaky and takes advantage sometimes when he is trying to snooze by taking the opportunity to assert her dominance and mount his head! :roll:
The only time I intervene is when he is either sleeping or if he is ill and is unable to resist her advances himself. I don't do anything other than firmly say 'no Poppy' and gently push her off him and she gets the idea, if she approaches him again I pre-empt it and say 'no' and she stops and nuzzles him and lies down beside him instead.
The frequency and triggers for her doing it depend on time of year, how much they've been restricted - i.e. how full of beans she is and excited - there are many different reasons - sometimes she's excited simply because she's just woken up and is full of energy, and other times he initiates it by starting it too - neither of my two let the other mount so we have a few mins of honking and attempted mounting by both and they end up going round in circles and then just give up and hop away or lie down.
I have also noticed that Poppy does it when she feels less secure in her environment and very often this has to do with 'our presence' and how we fit into the bunny bond. It rarely occurs at night in the hutch but happens most in the sitting room that they spend most of the day in - and especially if we are in there too, esp me. As a female human Poppy may experience my position in the 'warren' as a threat to her dominance. She certainly does it more If I fuss around 'their' corner whilst they are in the room e.g. picking up mess and tidying up the litter trays etc. By keeping away from 'their' part of the room it happens a lot less often, so I expect there is some redirected dominance issues occuring.
The other thing to bear in mind is that the bunny being mounted 'controls' the situation by doing nothing....Nino does this....he ignores her and if she pushes it he gives her a quick nip or just suddenly turns round and stares at her and she gets the message. Buns are pretty capable of sorting their own relationshp issues out - we just leave them to it.