Old Shame: GW regards the Squats and Zoats as "things better left forgotten." However, hints of them do pop up in new material from time to time...
Promoted Fanboy: Matt Ward is an infamous example. Every Codex he's touched has had it's fluff tortured, turned into Mary Sues, turned into a tabletop sweeper or any combination of the three. The only codex that he wrote that isn't universally despised is the Necron codex, and that's because there were two editors to keep him from breaking the game and the fluff. Despite that the Necrons still had their ancient Egyptian influence heavily Flanderized.
The Sisters of Battle codex that he wrote had the opposite of the usual problems. Though Games Workshop prevented him from having all the sisters get massacred all the time in order to fuel his obsession with sexist snuff-fics he still whacked the sisters with the nerf bat until they were a fine paste.
Shrug of God: Games Workshop has deliberately left everything regarding the two "missing" Primarchs open for fan speculation. Ditto for other major characters, like Commander Farsight.