I usually struggle to understand the root cause when one e-mail fails tu be processed.
What I do in those situations is to read production.log and search for "MailHandler:" entries.
It is not unusual to find only one entry, saying:

MailHandler: Message  cannot be processed

So I started this improvement, which already allowed to find out that, in a given case, the issue could not be created because the user didn't have permission to create it under that given project. In fact, the user had sent an e-mail to the wrong recipient (missed the sub-address).