WordPress has a serious problem with notifications. Don't believe me? Take a look at this page:
This is at the top of my list with WordPress frustrations at the moment. It's just poor UX. I get that we need some sort of notification system, but the problem is that WordPress gives too much freedom to plugin developers to easily abuse it with no limits.
That's why Notification Centre is my top plugin of the week. It's a nice simple solution to the UX problem, while keeping the notifications in tact and not just hiding them altogether. There's room for improvement, since it doesn't clean up all notifications, but you can't always account for every use-case in an ecosystem like WordPress's. Give it a try and you'll probably find some relief from getting dizzy with red, green, and blue messages every time you log in.