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Yesterday evening I opened my SO account and there was the red ball with a "1" at the top, notifying me about something new in my inbox. But when I clicked on "StackExchange" I saw on top only a comment I have already seen (the third one on this answer).

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But today when I opened my last answer on meta I saw that it got a comment yesterday afternoon, I haven't seen yet.

So, the red circle notified me yesterday evening correctly about a new comment, but that comment is missing in the inbox, and so I missed to read it. It is still missing in the inbox, so I think this is a bug.

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You can all your responses in your stackoverflow profile (Only you can see your responses).

If the comment is not listed there, it has been deleted by the author.

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There I can see only the responses on StackOverflow posts. The missing comment in the inbox, is a comment on a Meta post (listed in my Meta profile). But that doesn't matter, because the inbox is a global-inbox, showing notifications from all over the StackExchange network. I have been informed about your answer via my global-inbox, while I was visiting StackOverflow. – stema Oct 12 '12 at 21:33
And BTW, your answer has nothing to do with my question. The comment is there in my responses, it is below my answer, but it is missing in the global-inbox. – stema Oct 13 '12 at 18:27

Most likely the red circle notification was triggered by a comment that was deleted shortly after. There was a change recently that clear the red circle in such a case but I think that back when this question was posted it wasn't in place yet.

Now as for the missing inbox item, it happens. Not often but not very rare from personal experience I'd say that 1 out of 50 notifications that should arrive are going poof into thin air. Why? Probably server load, database conflicts etc.

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