Just a couple of days ago I've started noticing a strange issue:
I'd switch to Ripcord, see that lots of channels across different guilds each have 1 unread message; but then, when I open those channels, there are no new messages there.

I'm not sure if this is because moderators deleted a spam message or stuff like that, but something tells me it's not that, because for me this happened even in really tightly curated guilds.

There are various things that can cause this.

If you see it happen again, can you check to see if you also see the unread indicator in the regular Discord web client?