I hate code share with a vengance. Everything that happened to you and worse happens with code share. I have always managed to avoid code share and I'm going to continue to do so even if I have to pay a bit more.
The problem is that code share is not obvious to Mr J Public. Like the OP I was fooled by BE in a similar situation via BHX.
I bought a GLA-BHX-CDG ticket from BE but because the BHX-CDG was operated by AF I could not check in online for both sectors. To add insult to injury, there is no transit lounge at BHX meaning on arrival I had to exit to landside, walk back to check in, queue to show my boarding pass and undress again for security. The same process on the return journey.
None of this rigmarole was mentioned by BE at booking and email complaints to BE have produced only Standard Reply 2A/1 from customer service. This is dishonest behaviour and obviously BE have not thought this through