It's not a matter of break-in, it's a matter of Glock not machining their slides correctly. The extractor cut-out wasn't placed precisely so the extractor isn't holding the spent casing to the breech face. Glock has a new ejector which changes ejection enough to fix the problem, but they're only putting the new ejector into Gen4's. Both recent production Gen3's and Gen4's in 9mm and .40 have the same issue, it's not every single gun but a good number of them.
Call Glock and tell them what you experienced with your Gen4. Tell them you heard there's a new ejector to fix the problem and you'd like them to install it. They'll want you to send the gun to them so they can install it, be sure to ask for a prepaid shipping label if they don't offer one.
While they have it they'll check to make sure the extractor moves freely enough as well, for the last year or so their extractors have had widely varying tolerances, some fit too tight and can cause ejection problems as well.
You're lucky yours is a Gen4, I have a Gen3 G27 that has the same problem and Glock won't install the new ejector into Gen3's. I have to wait until the new ejector is included in the newest Gen4 trigger housings sold by online retailers so I can put the new ejector into a Gen3 trigger housing to fix my G27. Us Gen3 owners have to fix our own guns.