It started with this Document Library that contains important documentation. A group of people should be subscribed to it and alerts should be sent whenever documents where added, modified, or deleted. That's the easy part. I used the "Alert Me" in the "Actions" menu of the document library.
More libraries where added to the site and more alert subscriptions where requested. I bumped into the problem were I don't know if the user is actually subscribed to the alerts. Every time I go on and browse the "Alert Me" page and I get an empty users field! Ironically if you add the user again, he will get another alert, and if added another time, he will get it 3 times! The same alert email.
In the Settings page, we have a "User Alerts" management functionality which shows each user subscriptions to what document libraries, so if you have duplicated alerts, this is the place where you can delete them.
After deleting the duplicates, the user will only get 1 alert per each document library. You have to take into consideration that "User Alerts" management covers document libraries/ lists per site level, yields you have to go to each site settings and delete the duplicates.