If I may jump onto this topic:
Is this a similar problem with the itinerary I was playing around with?

hnd-dfw-lax-jfk-hel-agp-mad-lhr-doh-ktm-kul-cgk-hkg-cts-hnd

It would also give me errors saying too many stops in continent of origin, I am understanding it correctly, that it treats KTM, CGK and CTS as stopovers even if flight "connection" in KTM would be below 24 h?
(Plan would be to only have real stops in CGK and CTS, other Asian cities just connection points).