Hm, there should never be more than one issue for a certificate per user so sounds like there was/is a bug in the code. Glad you got it sorted and appreciate your help Shirley. If you ever discover how this situation came to be please file a report at https://github.com/mdjnelson/moodle-mod_customcert/issues with replicaton steps. Thanks!
Custom certificate (plugin)
End-user unable to download Certificate
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