If the latest message in a channel has been deleted, the unread message flag is still set until you move the marker past it

[tigerbears]

User A reads all their messages from User B. User B sends a message, then deletes it. User A's channel will say it has unread messages until they view the channel and then, only if either a) deleted messages are shown in the channel or b) clients do some bizarre special-casing for setting the stream marker when deleted messages are involved.