Let’s say you have a private conversation with a member and the appropriate topic /t/[topic-name]/[numbers] is open. Now the member will send you a new message in this topic. The green indicator for new private messages (on the Avatar) goes to (1). You directly see the message in the topic, since it is already open. Now you switch to another topic and the green (1) is still there.
I don’t have a consistent way to repro it, but it happens quite often to me. There’s definitely more to it then requiring to actually read the post, when it happens to me scrolling through the post doesn’t help.