I am running SiteScope 9.0, and have made a handful of changes over time. That said there is an old group with a few old alerts, all of which have been deleted, that are still firing! Any way to trace these to something and permanently remove them? They are nowhere to be found in the web UI and these are throwing LOADS of false positives now.
It's been ages since I've played with SiteScope 9, but I'll see how much I remember... try checking in the \Sitescope\groups\master.config file and see if any alerts are still defined there. If not, look in the .dyn file for the group that's sending the alert and see if it's still defined in there.
Unfortunately, the web interface can be a bit flaky at times - I still have similar issues with version 11.12, although it's better than it used to be.