I bought an AY ticket a few months back for roundtrip flights totally operated by BA. The translant was an AY codeshare, but the EU flight was just sold as a BA flight number. Neither BA nor AY let me check in online & upon arrival at the airport, BA didn't initially see the full itinerary (BA thought I was stopping in London).

What gives? It's the same PNR on both airlines with all flights operated by BA, so why is BA having trouble viewing the itinerary?