These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The 7th Edition Codex at least attempts this by retconning the notorious Khornate Knights incident to exclude any mention of the Sisters of Battle, as well as showing the Sisters as brave warriors respected by the Grey Knights in other lore.
It also removes the notorious Game Breaker Plasma Siphon entirely and tones down several of the most unbalanced options the Grey Knights had in the 5th edition codex (However you can still use with for Inquisitor allies).
Their Marysueness has been downplayed as well. Casualties are heavy, resisting the warp corruption is difficult, and at least one case of defeat is described.
Base Breaker: The 5th Edition codex has a great many people wanting to murder Matt Ward by his retcons of the chapter, various internal What the Hell, Hero?, and his apparent losing of the plotline regarding Chaos being The Corruption.
Canon Defilement: Sweet Emperor of Mankind, even C.S. Goto had a better idea of how Warhammer worked than the guy who wrote the fifth edition codex.
Ensemble Darkhorse: Castellan Crowe was regarded as the best thing in the 5th editoin codex.
Game Breaker: The Plasma Syphon. A weapon which makes any plasma weapon useless against a unit equipped with it. The problem was that some players began to take the fluff into account and apply it to anything based plasma. Complaints were made to Games Workshop who ignored these letters. When the FAQ was released amongst the many leaps on logic it was confirmed that the weapon made anything related to plasma useless. Tau players are now refusing to play anyone with Grey Knights as 95% of their weapons are based on plasma technology.
Magnificent Bastard: Alaric becomes this at the end of the Omnibus, seriously, who could have managed to fool not one, but three greater daemons along the series, or make a plot to take down an entire daemon world and the chaos lords at its command? And all of this while fighting through hell and surviving numerous Mind Rapes?
Misblamed: Some people have noted this about Matt Ward's 5th edition codex. While Ward is credited as its writer, the writing team has admitted they collaborate to a degree on codexes, and several of the most infamous bits of Ward's fluff (particularly the Khornate Knights incident) are due to Ward implementing 2nd edition-era fluff rather than them being entirely his own invention.