When messages are sorted by the unread flag, replying replies to the wrong message.
If you click on an unread message, it is marked as read, and in the case of sorting by the unread flag, moves to the read portion of the message list. Clicking reply at that point then replies to the message that is now in the position that the original message was in, instead of replying to the original message. I first reported this in 3.5.1 via an e-mail, but it's still present in 3.6.0. It happens in both Linux and Windows versions of Sylpheed.