As we've been digging deeper and deeper into the cavern that is old Gas Cubby code, we've uncovered that the current version of GC has been keeping logs of ALL the user's data. So it would be safe to assume that if you had 10 reminders, synced, then later deleted 5, synced, those 5 you deleted were still retained somewhere in the sync data.
I believe this is what may be triggering some of those mysterious notification badges. The reminders aren't active, but there may be remnants in the sync data that's triggering the badge (and therefore keeping you/us from deleting it).

Good news, we're cleaning that up and wont be using the logic old(current) Gas Cubby uses. With the new update the mysterious badges should not be displayed(stuck) like they are now.

In a few days I may be reaching out to a couple of you in this thread to dig into your backup files and view it in GC 3.

If you need someone else on your beta list for v3.0 or need an extra exported log, let me know. I'm experiencing the same mysterious notification badge icon and have a background in system testing.