Anyone know how I can fix this? Phantom message alerts. Solved

Check in your settings whether you have disabled the visibility of bot responses. This can happen if bots replied to you and your settings are set to not see them.

have you checked messages? Atleast I have that problem in jerboa that even though I am in the Inbox seeing "all", the app doesn't present to me my unread messages.

If the msg is real you should have a notification and you can click it from there

I also don't think that notice icon and actual msg are not synced at the same time. Ie message might come through later.

Happens to me too, but it usually goes away in a few seconds or in a refresh. Probably browser cache dependent.

Try doing a factory reset on your phone.