Did I mess up by doing that and create a situation like that?
No, this is standard procedure. Your system and software have been updated to the latest, stable version. Unless you actively add a repo containing unstable software versions, there shouldn't be anything to worry about.

You really only need the "CD ROM" repo for the base install from physical media; maybe there are edge cases where you'd want to roll back, but on the whole you're in safe hands with the official, Debian stable repos 🙂
Enjoy the Linux journey! Debian is a great starting point to learn from, IMHO.