OsTicket will create an internal note when an agent is replying to the alert / notification mail. This is part of the osTicket concept -> use the web interface to reply to the end user.
The reason for this behavior is simple: When multiple agents receive the alert / notification mail and every agent would reply to this message, the end user would receive a lot of different replies from different agents which would may confuse the end user and/or is leading to chaos. To avoid this, the agents should always use the web interface to reply to the end user, so that the other agents see what was already written back to the end user and don't reply to the end user again and again even though there was already a reply from a different agent.