There is a record that is in a non-Global domain, e.g. TOP/xyz.
An email notification is sent by a notification that is in the Global domain. The sending conditions in the notification have all been met.
It may have been expected that the email would not be sent since the affected record is not in the Global domain, but the notification is in the Global domain.
This is working as designed.
The documentation is not clear on how this should work:
This use case is not defined under "How domain separation works in Notifications". A request to update this documentation has been entered.
The documentation here should make it clear that notifications in the Global domain will be applied to all records no matter which domain they are created in.