What really bugged me...Negan is a damned ballistics expert. "That's a home made bullet!" Even if I accept he knows that much,....why would he assume so much as to even look at the casing? More likely he'd think they had ammo stashed somewhere. The simplest answer would be think Rosita found a bullet or hid a bullet.
Yeah, this kind of bugs. They find guns, medicine, and all sorts of crap all the time. Like someone couldn't have found a reloader kit, some black powder, and melted some fishing sinkers for a bullet. It doesn't need to mean that they've got some kind of professor capable of creating this all from scratch.