Normally it will go away on its own. It's happened a few times to me before, and currently is doing the same thing for me. andrew (Our Supreme Lord and Overseer) has said before that it'll work itself out, here.
Ahh alright, cool. Sorry about that
The ghost notifications are spam posts that get auto-flagged and automatically hidden, and automatically delete themselves every night. We don't immediately delete because a lot of the spammers just instantly re-post as soon as they notice the post is deleted (and instead just hide their post from everyone except themselves), but this unfortunately causes some ghost notifications sometimes, especially in weeks (like this one) were we get a few hundred spam posts.
I'll experiment with a quicker auto-delete since I'd like to avoid having things like a captcha on signup. Thanks for letting me about the problem though. :)