EK regulars probably know this much better than I, but their website seems to calculate miles/routing/stopovers by one set of rules while booking. Once ticketed, it's almost like the itinerary is re-examined and different rules applied.

Where I always see it happen is booking a <24h stop in DXB, by searching a three-part itinerary, ex: LHR-HKG, HKG-DXB, DXB-LHR. After ticketing, this shows as a two-part LHR-HKG-LHR with a connection.