Running find or rsync over a home directory on macOS 10.14 and later produces a stream of 'Operation not permitted' errors on paths such as ~/Library/Mail, ~/Library/Messages, ~/Desktop, ~/Documents and ~/Downloads, even though ls shows the user owns them and the mode allows access. This is Transparency, Consent and Control, the privacy subsystem, denying the request because the calling application has not been granted access.
The permission attaches to the application that owns the process, not to the Unix user, so Terminal, iTerm2 and each IDE are governed separately. A script run from a launchd job is attributed to launchd or to the job's own binary.
Grant access in System Settings under Privacy and Security, either the specific category such as Full Disk Access, then restart the application completely so the new grant is picked up. For automation, note that a signed application's grant is tied to its code signature, so replacing the binary revokes it. Backup tools that skip files silently rather than erroring are usually hitting the same wall.