Even fixed rabbits have dominance issues, it's just less. Rabbits in a group have a hierarchy. There's always the potential for minor squabbles, nipping, and chasing. As long as the subordinate buns know their place and it doesn't break out into a fight, this is all normal behavior. I have a group of 7 and the boss bun chases and nips at the lesser buns when she wants them to move out of her way. As long as they move it's not a problem(and they do move), and at the end of the day they still groom each other and snuggle together.
So for the litter box issues, I think you need to restrict your groups freedom for a while. No bed, no rugs, nothing soft, some rabbits can't resist peeing on soft things. And you may need to also cut back on the floor space they get too. Use xpen panels to block off your bed and restrict their area. They were probably given too much space too quickly, without those litter box habits being set first.
I would also provide more litter boxes, at least for now(some may be removed as litter box habits improve). As many litter boxes as are needed to make sure they are always using the litter box, including filling up the whole floor space of their area if needed. Then after a few weeks, remove one litter box and see how they do. Start by removing the least used litter box, one every few weeks as they are consistently using the litter boxes. and not peeing outside of them. Til you are left with only the most used litter boxes, maybe only two so they have a choice of which to use. The problem you may be having is the boss bun is hogging the litter box and the subordinate bun needs to pee but isn't allowed in the litter box. So they need more than one to chose from in this case.
I would also suggest a change of bedding/litter unless you really like what you are using now. I've found wood pellet litter to be the cheapest and best at absorbing urine and controlling smell. Plain wood stove pellets(I prefer pine/fir over hardwood ones) work or equine bedding pellets(what I use now) are both the cheapest options. Or there is feline pine at pet stores if you don't have access to the other two. It's just not as cheap.
I like to make it 1-1.5 inches deep so the urine drains away and is covered up well by the top layer of pellets(also helps control smell). Then make sure the pellet litter is topped with a soft layer of hay as some rabbits don't like the feel of the hard pellets on their feet. And change out the wet hay at least every few days so it doesn't start to grow mold. Also making sure the litter doesn't get too soiled or wet. Some rabbits will stop using their litter box if they feel wet bedding on their feet.
I think your bedding may be getting too wet(just from looking at the photo), and they also need a lot more hay covering the bedding. They should always have lots of hay to pick through and the leftovers get left as a layer covering their bedding is how it should work. Hay makes a good cover for the bedding to keep it in place, drain urine away, and lock in the urine odor under the hay(consider it part of the bedding/litter). If hay cost is an issue, I would suggest going to a feed store(if you don't already) or reliable hay farmer, and buying a bale of good horse quality grass hay(no mold, no noxious weeds, low dust). This is the most affordable way to provide lots of the needed hay for rabbits. Buying bags from pet stores is so much more expensive.
So I would try these changes and see how it goes.
https://rabbitsindoors.weebly.com/litter-training.html
https://rabbitsindoors.weebly.com/odor-free-home.html
http://wabbitwiki.com/wiki/Litter_training
http://wabbitwiki.com/wiki/Litter_Training_FAQ