EU changed a lot this year (EU EES and ETIAS, long delayed), so this is probably different now than it was for some people before. It should be passport + biometric in and out, with a passport and biometric enrolled once as well, and visa-free stay duration (and other activities, like criminal stuff) logged against that record as well. Previously if you entered in one country and exited in another there wasn't really any closure of the record, so they effectively didn't care, and you could stay in EU indefinitely (and enter/exit much more while also overstaying, especially if you had multiple passports or could enter/exit from different countries).

> Granted I was using my US passport, not my EU

Then you're American as far as they're concerned. Citizenship isn't something you can tell at a glance or determine by measuring a person.

Thats why. You don't have to go thru this extra check if you use EU passport or if you have temporary/permanent residency (but not travel visa) attached to your passport.