That's sometimes true, but not in this case. He knew how good the sessions were for Sister, I'm a Poet, Disappointed and Will Never Marry and immediately boasted about them to the press. They were simply recorded too late to make the album.
I agree that Roy's Keen was a mistake, but ironically the same thing happened with the b-sides as with Disappointed. A real shame that Lost and The Edges are No Longer Parallel were again recorded too late to make Maladjusted.
Sometimes, of course, he feels that the b-side just doesn't fit the vibe of an album. Other times, as you've said, he simply makes an error of judgement.