The contours were all created from a consensus of participants contours submitted to the main AUTO-RTP challenge. Therefore, the error does not come from applying margins directly, but from the application of margins by various participants. Some participants only used a PTVp_6000 for planning, and did not provide a structure for the inner PTVs - consequently their structures will have influenced the PTVp_6000 and not the other PTVs leaving to the overlaps. One participant submitted the PTVp differences as the PTVp regions i.e. the PTVp_7100 was actually the PTVp_7400-PTVp_7100. This also resulted in the PTVp_6000 not being as anteriorly as it should be.
The question is what to do about it. I could take the PTVp_7400 consensus (or appropriate for the other structures) and apply my own margins. Or, I could choose the "correct" participant contours and form a consensus from only then. This would however change the input contours for this challenge. I'm open to suggestions as to what the participants would like.