This can happen if the email client doesn't properly set the headers when sending out a response.  There isn't much that can be done about it most likely, as it is a client problem.  It can be looked at if you can reproduce it reliably though.

WebGUI didn't append the original post to the wrongly-created thread, the user's e-mail client did.

Hiding a tag would not work since some people do not include the entire original message when replying to a CS post by e-mail.

When you reproduce this, look in the database, Post table, originalEmail column. The e-mail must have an "In-Reply-To" header in order to be detected correctly. Attach the contents of that column to this thread with your reply and we can see if this is WebGUI's fault, or the fault of whatever MUA is sending the message.

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I've dug a little deeper about the subject, and it seems there is also a "References" header that may or may not contain parent message Ids.

The correct interpretation of RFC822 is to use In-Reply-To, and that is what we do. If this becomes a very large problem, we may have to look into what we can do with the References header.

Closing until more information.