Zeb is seen climbing out of a storage crate, leaving Chopper still inside. Given how much room Chopper is shown to occupy, there wouldn't have been enough space inside for Zeb as well.
Chopper is unable to extricate himself from the storage crate used to smuggle him (and the other Rebels) into the Imperial factory, even after the lid is removed. Chopper has a rocket booster on his underside and has been seen flying unaided many times.
Kana tells Ezra that he wouldn't understand what the clones are like because he wasn't around when Order 66 was carried out, and wasn't even born yet. While it's true he'd have no memory of those events, it was previously established that Ezra was born on Empire Day, the day that Order 66 was carried out, so he was born when it occurred.