Except I had a similar issue, and it was with AA blaming AA!

Well, first of all, early morning in OSL, BA couldn't issue me my AA LHR-LAX second leg board pass because they said AA Worldwide was down. (But once they decided to only print the first boarding pass, they had no problem printing it without communication with AA Worldwide despite it being an AA codeshare.)

So when I got to LHR and got through the FCC to the AA agent in T3, he said "oh, this was booked with AA in the US" (of course, that's where I live!), and he said it was all wrong, and had to type furiously for several minutes to get my boarding pass printable. He implied the SWU had been applied wrong, but I had requsted an SWU in both directions, and the one two weeks earlier had worked no problems (starting from the US). He showed another agent that it was showing "two coupons applied" or something like that.