We are encountering a bug with the Completion Certificate plugin…
Is this the Custom Certificate (mod_customcert) plugin? If so, which version?
…in our Moodle environment…
Which Moodle version?
…have confirmed that the scorn script for this certificate emailer is working correctly…
That doesn't sound like mod_customcert, but if you're using SCORMs there is an unresolved bug with activity completion in Moodle 4.3 (MDL-79967).