So, this was probably my goof but we have a 4 digit extension setup. Without thinking I made extension 0001. 3CX gladly accepted it and it's able to be called if you dial 0001. There also doesn't seem to be any negative effect on the rest of the system either. However it does NOT show in the extension page in the management console. If you export all extensions it will be shown where you can recover whatever information you need for that extension.
This is mostly just a bug report since I don't know where to put it and also asking if it's possible to remove the extension even though I can't see it.
EDIT: I'm just dumb. Needed to clear browser cache and relog