Did you use a plastic, brass or steel cleaning rod or patch eye? This may have expanded and/or deepened the primer pocket, created the ding, and caused the primers to seat further into the primer pocket.
I recommend you get a primer pocket cleaning tool or use a long nylon bristle brush to clean the primer pocket rather than a cleaning rod and patch.
This once fired brass is it military issue or commercial ammo?
Military ammo generally, but not always, has a primer ring/bushing. You'll need a large primer pocket reamer to remove it or purchase large rifle military primers. I have and you can, use a razor knife in place of a reamer, but IMO&E use a primer pocket reamer.
I suggest you only charge and seat a bullet on 10 randomly chosen brass. Go to the range and see how well they work.or don't. If they work no harm no fowl reload the rest of your prepped brass. If there is a problem, you caught it early and can rectify it.
Just my 2 cents.