That might explain my situation last weekend. I checked in at SAN and the AA check in clerk asked if I had Verifly. I stated that I had tried but Spain was not a valid destination for BA on Verifly and if I added a trip to Spain from the US, it expects me to fly direct between the US and Spain and that a U.K. trip from the US to the UK fails as Verifly would not allow me past the 2 day test reference number. I showed my docs and was given my 3 boarding passes, including the BA LHR-ALC one.

Upon landing at LHR, I opened the BA app to try downloading an electronic copy of my ALC boarding pass to avoid rooting around in my bag. The app indicated that I had not yet checked in for the flight, even though prior to leaving the US, I had successfully uploaded the docs in MMB and had been given the all clear and I had checked in at SAN

I stopped off at the desks just before the connections e-gates and it took the agent about 5 mins to fix whatever the problem was.