Has anyone had an issue with duplicate JE#? Our settings have it set to warn/block, but I do notice the auto-numbering was set to allow override. However we discovered there are a couple JE# with the same number

Not specific to JE. IF the transaction number is generated when the user open/copy multiple at the same time. Is your combination of block but allow override the issue? Usually after I’ve completed a migration I remove the allow Override.

I was wondering the same thing. I am guessing they set it to override back when they did the integration, but never turned it off. I tried testing in sandbox, but was getting blocked. It seems like a random occurrence that's different to reproduce.