Is it possible that there is an action rule that includes a step where this user should be getting an email?
The same thing happened where I work. Eventually I opened up the Alerts (basic and advanced) and looked at all the actions assigned to each one. I found the list of users receiving the alerts and adjusted it.
Still more notifications were going to employees who were left.
I found more rules with triggers and actions in the syslog section.
Once I cleaned those up, all was better. Hopefully you'll find the users to remove in those Basic and Advanced sections, but you'll need to open every alert and inspect each Action.
Don't forget Kiwi can have alerting rules in it, too--if you have Kiwi.