If you receive a meeting/appointment request and reply to said appointment, the person who has scheduled it will receive a reply but it will not be associated with the original event.

To reproduce:

 * On one client, create an meeting and invite a second person
 * On second person's client, select "accept with reply" and send them the confirmation
 * On first client you will see the response but it won't correspond to a calendar item.

I spoke a bit with mcrha on #evolution about this, and the suspicion is that the UID is getting mangled somewhere, such that the UID in the original calendar item and the UID in the response are not the same.