All important questions. The answers to these could really help. Without this information I can only guess at what might possibly be going on, but the bottom line is that if no one is getting hurt, no one is getting hurt.Did you get your rooster at the same time you got your hens?
How old is your rooster and how old are your hens?
What actually happens at roost time? Do the hens go in first and the rooster waits outside, or at the pop door entrance?
Does your rooster mate with any of the hens?
Bedtime can be disruptive in my flock. Some flocks are better about that than others. They all want to sleep in the prime sleeping spots but the ones higher in the pecking order get those. There can be squawking, bumping, and shoving as they sort it out. Occasionally one is knocked off of the roost. But no one gets hurt and they eventually sort it out. Life is good.
Even with further information my suggestion is most likely to be the same as some of the others. Give them a chance to sort it out. The first time you try leaving him in overnight, be out there at first light when they wake up and see how it is going.