Why is an agent or mailbox included in the Conversation Logs if it should be excluded based on the active filters?

The Conversation Logs will always show the full email thread and all of the emails in that thread. This allows for each of the emails to be viewed in context and for you to follow the thread more easily.

The filters are excluding those emails in the threads/conversations from the performance statistics e.g. average First Reply Time at the top of the Conversation Logs report.