For what it is worth, I experienced this with a couple of browser tabs I had left open prior to the XF2.2 upgrade - the contents of those tabs were for two different threads and still with the XF2.1 editor. I haven't seen it happen with any newly opened XF2.2 browser tabs. It wasn't until after browsing through the XF2.2 updated XenForo community and returning to these still XF2.1 tabs did I notice any '0' alerts badge.
Whatever caused it seems to have happened during or not long after the upgrade, but I don't know .