I'm sure that it does happen. It would be simple to pick one up in any situation and accidentally work it into the priming device. I believe that nobody is so fastidious that they don't have a used primer floating around on their bench or floor on occasion, and it wouldn't be that far away to drop a live one and mistake a dead one for the lost one. There should be a whole lot of checks and balances, however, that would keep it from going into the chamber of a gun. I personally have at least three. First, I check the box as it is opened, I load them into the tray and when closed, I verify that every one of the primers is bright and new, I try to look at every casing head to verify this as they are being primed, and If I forget that, I still always feel the thing with my index finger to verify that one went in. In any case, you'll notice if the primer wasn't inserted by lack of pressure.
Last step is boxing them up. Bullets down in a rack. Once you are there, you're finished.
There shouldn't be any rounds at all in your entire kit that isn't complete. Dummies should be left with empty primer pockets.
A while back after several rounds of sorting I put a .380 case into my 9mm resize die. I'm not really sure how it happened, but that's as far as it got. There were at least a half dozen steps after that that would have showed the error.