Have crushed a few primers against the case but not had one go off yet. Sorting is the only method I know to filter out the wrong pocket. The last batch of brass I bought from the range, I sorted through once then cleaned and sorted while removing from the corncob again.
I did find that realigning the shellplate & primer feed mechanism on my 550 makes it a little easier to get primers nice & centered before pushing them home.
I'm a whole bunch more careful with them now though. If in doubt, case comes out.
Someone posted it earlier, but I find when I sort brass my eyes I guess get tired and small and large primer holes start to look real similar and it gets hard to tell. The idea above about the reaming tool is a good quick idea.