This might deserve to be closed; it seems to be a bug, but a very, very minor one. The conditions under which I observed it were rather specific. I'm not sure which of the conditions were important, and don't know how to test them jointly or in isolation; but maybe someone who reads MMO can. This is in Safari 16.3 in macOS Ventura 13.2.1.
I viewed the revision history of a post. While I was viewing the revision history, a user @-notified me in a comment, so my mailbox got a red 1 icon. I used the back button to navigate back to the previous page, at which point the red 1 icon went away, I guess because my browser was showing me a cached version of the page.
Despite the red 1 icon not being present, when I clicked on the mailbox, the new comment did display in my mailbox. However, I could not click "Mark all as read".
By contrast, this is what I see under normal circumstances:
This is very easy to fix (by clicking on the comment text itself to go to the comment, or just reloading the page), but it is probably unintended behaviour on a rarely exercised code path.