Sadly, the sex ratio of your flock is one problem. Its commonly said that you need 4 or more females for every drake. There are exceptions to that. My son's flock of 2 females and a drake were happy and the drake rejected a third female [daft duck] although the third female gets on just swell with the girls.
Then drakes get hormone surges in the spring. My drakes are coming up to one year old now and, having cohabited really well last year, started pecking and fighting in January. There is no blood, no big feathers pulled --- there is an occasional small feather and often down caught in nares of the aggressor. The ducks still want to be together and when I put a duck that has been particularly aggressive in a dog crate for time out, the others stay right by the dog crate with him until he is let out [after about10 minutes]. In the coop, there is a definite pecking order for access to food. I am learning to accept this behavior as just boys tumbling with boys being boys. I have introduced a 4th drake this month [actually the drake from my son's flock who was attacking the new female.]
You can stop the aggression in the coup by putting the bad boys in dog crates overnight, inside the coop so that they have the company of the other ducks but cannot attack them. I have one drake sleeping in his own dog crate inside my coop. He is a small Pekin and also the most bossy drake. He gets stood on by my muscovy drakes when they tire of his constant badgering and jabbing with his beak. He loves having his crate and waddles straight in there at bed time. That crate is 20" by 30", two door retriever-brand crate from
Tractor Supply. He is a small duck. My time out crate for the bigger muscovy drakes is 24" x 36", also a 2 door retriever-brand.
However, it your drakes can see/hear/smell the female ducks just keeping them in a separate compartment or a dog crate in your coop will not work.
I think you have to make a difficult decision -- and resolve the sex balance.
It is easier to rehome females. Few people want drakes and there is surplus available because of the sex ratio issue. However, some people like me, only have drakes and get great pleasure from them.
If you have a large yard and the additional resources for a second coup, having two completely separate flocks might be possible [like my son and I although our flocks, while related, are in different back yards.]