Edit (2023-02-06): The problem persisted and I found the real fix. I have an “original” Ergodox EZ but the configurator defaulted to “glow”.
Choosing the “original” model fixed all issues.
Old fix (which I still kept): It’s the first time I was using my Ergodox EZ with my new MacOS setup.
After flashing the keyboard with a slightly adjusted layout, I started experiencing issues. The Ergodox EZ ignored keypresses of the same key when twice in a row. The keyboard dropped keys randomly when I was typing fast.
In those 4 years without updating the firmware, they must have changed the default debounce value.
Lowering the value from 30 down to 5 using the web configurator fixed the issue for me.