I wouldn't worry a lot about the enlarged hole. I'd bet real good money that it was like that before you loaded the round, you just didn't notice it at that time. The hole was probably caused by a defective punch at the factory. At first I thought you might have had an NT (non-toxic) brass case in the lot which does have an enlarged hole by design, but it doesn't appear that is the case. It will change the ballistics of that particular round slightly, so you can discard it if you wish. I wouldn't.
The 'cratering' you noticed on the inside of some cases is normal for mass produced brass. It is the small flaps of brass (for lack of a better term) left when the punch makes the hole. Some reloaders remove it with a flash hole uniformer which simply grinds down the metal surrounding the flash hole inside the case. For general use brass, that isn't necessary.