If you read previous threads about the companion certificate you'll see that 'misbooking' seems to be common. I remember one post from Spring 2001 where the poster said that not only was his wife (companion) able to be upgraded, but that she also received miles for her flight, and to boot, double base miles because it was during the promo.
Almost sounds like the 2nd ticket is booked in a paying fare class, which you'd think with the computers should be allowed.
Jeff