I am an admin for an mtGenome project.
Recently, me and a project member found out that mtDNA extra mutations were shown differently for me and the kit owner. For me, only the fylogenetically rejected (that is, too labile) mutations were shown as extra mutations, whereas for the kit owner also her two extra CR mutations were shown.
This is a minor bug, but when there are other open bugs in mtDNA area (concentrating in GD calculations?) this might offer a clue what is going on.