I thought this had been fixed, but there was/has been a bug with this feature from early on when it was introduced that would randomly show inaccurate results. We stopped using the feature a while ago since wasn't reliable. Its possible its still an issue that needs to be addressed though.
We're aware of the issue of Self Service badge notifications not always showing the correct notification(s) number.
It's filed under PI-000865 and is still in an open status, which means you may see the behavior manifest in your environment.
If you haven't already opened a case with your TAM for this, you can get in touch with them to get a case opened and attached to PI-000865 by either giving support a call, sending an e-mail to firstname.lastname@example.org, or by using the My Support section of Jamf Nation.
@amanda.wulff Is there any update on this? The notifications framework for Self Service is all but unusable still in 9.98 if the App badge isn't going to work correctly. Seems to be a ton of PIs lately that are not being prioritized for close. We can't all wait for 10 to hopefully fix a lot of this stuff... I just enabled Notifications for Self Service on my dev box, enrolled a client, and instantly I have 9 phantom badge items, and clearing out the Self Service plist and rebooting does nothing.