Sometimes clicking "Reply to Thread" will Reply to the message a user just replied to instead of to the thread. To reproduce:
1. Go into a thread with multiple messages
2. Click one of the "Reply" buttons for any given message, so that you are replying directly to one of the messages
3. Enter your reply and click "Post Message"
4. You should now be back at the main thread page, click "Reply to Thread"
5. Notice that you are now replying to the last message you replied to instead of to the original message for the thread