If you have a keyboard/mouse/autohotkey macro that sends the 'use' button very quickly you can dupe chickens. It happens in single player and on a server.

Example video here

Minecraft: 1.12.2
Forge: 14.23.2.2624
Roost: 1.12-1.2.0

Adding a delay to the Chicken Catcher (similar to ender pearls') will fix this issue.

the duped chickens disappear after interacting with them when it happens to me. I use shift+click to move them from the breeder to inventory, and when doing that you'll see one of the two breeder slots retain the chickens and send them. you can then grab them again and it looks like a dupe, but when you try to pick up the duped chickens they'll disappear. you might be seeing a different behavior, but that's how it works for us on Roost 1.12-1.3.0

This can happen without a macro too, I've triggered it by simply clicking fast as the chickens are running around and I'm trying to catch them I spam the button.