I love Chicken Run, as well as all Aardman movies. With that disclaimer, on with the silly observations:
Who’s the father of all those chicks we see at the Chikin Sanctuary at the end of the movie? Logic would say Rocky, but perhaps piloting the airplane gave Fowler an ego-boost and he found himself able to perform with the hens.
There are a lot of chicks. The roosters would have to have multiple partners, despite Rocky and Ginger’s pairing off.
After the pie machine blew up, Mr. and Mrs. Tweedy would have to fall back on egg-farming again. Another whole batch of hens are due to be held prisoner in the ovo-concentration camp!
The thieving rats had tunnels to the chicken run, to bring in the stolen goods. Why didn’t all the chickens use the rat tunnels to escape?
Truth be told, I was kinda curious about Rocky’s sleeping arrangements before the escape. He looks for a bunk and multiple hens wave eagerly at him, and yet he ends up tossed out to crash with Fowler. WTF? Is Ginger such a prude that she’d, heh, cockblock everybody?
I took it for granted that Ginger didn’t want anybody going broody or (worst-case scenario) having to cope with baby chicks before or during the escape. As noted in the OP, chickens don’t seem to do the birth-control thing.
So when Rocky says “Hey girls, how do you like your eggs in the morning?”, Ginger’s response is “Unfertilized”.