Unless this is being affected by a different issue, I believe that accounts I have filtered on discord (which are mostly bots) will still increment the unread badge for a channel.
This just makes it a hassle to check a channel for a message only to find no new content present

It shouldn't, I think. There is an issue currently with Discord restarting their gateway servers frequently: sometimes the unread state won't have been recently synchronized to the server (due to some dumb & conservative code in Ripcord) and it will re-sync back the old unread state from the server upon reconnecting, causing unread badges to reappear for channels which were already read. Whew, that's a long sentence. Do you think your issue might be that, instead?

Yeah, I wasn't able to replicate the problem when trying on some test accounts, I will assume this is some well timed gateway reconnects and close the issue