OK, here is the way it works.
You get 2 new emails. You get a notification in the Action Center that you have 2 new mails (notification center has multiple pages to show TONS of notifications).. You clear the notifications, the tile still states you have 2 unread mails. These are completely separate and not connected together at all. This would not make sense for MS to try this as each app has it's own notification settings. You actually have to go into the app to clear the tiles because that is how the app knows you have at least looked at them (or opened the mail program that allows it to know to clear the tiles). Try to get action center to clear itself AND the tile would be too much work for MS to take on with all of the different apps that are allowed to send notifications.
Now, you can tap on the notification centers notification for mail and open the app and clear the tile that way.