This series has a very controversial one of the Jedi Order. The Jedi Knights have severed themselves from their families and made use of a slave army in order to protect a Republic that's obviously not worth protecting. As a result, they're individuals who deserve nothing but scorn and derision. Skirata reflects on this in Order 66 and calls his motley crew his "syndicate." He thinks what they are doing is completely justified because they are saving millions of lives. Later continuity like The Clone Wars would Retcon this hard, stating that the Jedi did care and respect the clones, who executed Order 66 not because of their disillusionment with the order, but because they had been brainwashed to do so.
Ironically, Traviss' depiction of Mandalorians is itself an example of this trope; previous EU material had established Mandalorians as a race hated and feared throughout the galaxy due to being brutal warmongers who eventually took up a racial proclivity towards bounty hunting and mercenary work after their empire was shattered, who were responsible for the complete genocide of several species, and who sided with the Sith in every single Sith/Jedi war. Hardly admirable characters — and certainly not better than the Jedi.
Time has not been kind to the book's interpretation of Kal Skirata. Rather than the idealized Mandalorian father, fans have instead noticed that his sons have taken to going on missions that keep him as far from them as possible, that he named one of his sons (Darman) "Souless", that he knowingly put both Etain and her unborn child in danger in his harebrained scheme to hide the pregnancy from Darman, that he actively cultivated the idea that the Nulls were insane, on and on. The end result is that Kal Skirata ends up looking just as abusive if not worse than Vau, only through manipulation instead of violence.
Fridge Horror: Season Six of The Clone Wars revealed what Order 66 really is: a physical chip inside the head of every clone that drives them to kill Jedi against their will. In other words, in the official setting, it could very well not have been a Jedi who kills Etain when she attempts to protect a clone soldier, but Darman and Omega Squad, who would be forced to kill her via Order 66 and the implant, if they could not resist it.
Somewhat justified. Sadly Traviss rage-quit when she was going to subject her own creation to some very well deserved scrutiny. There was much foreshadowing in 501st that even the "safe harbor" on Mandalore (the planet) may not come free and without attachments. Mand'alore (the ruler) is just as political as the rest of the galaxy and would use the clones for his own "patriotic" purposes.
Mis-blamed: Whatever the series' faults, the 3 million clone troopers number wasn't one of them. That blame lies at the feet of R.A. Salvatore's Attack of the Clonesnovelization, movie-level canon which interpreted Kaminoan Prime Minister Lama Su's line, "200,000 units are ready, with a million more well on the way," as meaning 200,000 clones rather than a more sensible 200,000 military units (at least make it 200k companies!). Karen Traviss and others had no choice but to use it because, at the time, movie canon overrode EU novels. Post-Disney, a new canon reference book retconned "units" to refer to an entire division of clones (approximately 10,000-20,000 troops each).
Moral Event Horizon: Scorch views a mortar attack on a base's commissary as this. When he and the rest of Delta tracks down the guys that did it, he brutally kills them, then repeatedly pours blaster bolts into their bodies in full view of a gaggle of onlookers.
Out of universe, Skirata and Ordo murdering Padawans during Order 66 could also qualify.
Squick: The clones are only 10-13 years old in the books. No matter how many times the book stresses they are men and mentally and physically twice their age, there is no changing the fact that the clones have only been in the galaxy for 10-13 standard years.
They Wasted a Perfectly Good Plot: The storyline takes place during the same time period as the Mandalorian Protectors are supposed to be rampaging through the galaxy, even launching an attack on the clones' homeworld of Kamino. Do we get to see some more Mandalorian versus clone action? Nope. Do we even get a cursory run-through of the campaign? Nope. And by the last books, our protagonists are regularly teaming up with the last survivors of the Protectors without any tension about the whole "attacking our little brothers," or "wiping out almost everyone we fought alongside."
We do actually see some of this in True Colors, when Omega ends up stationed with some troopers who've been fighting Mandalorians aligned with the Confederacy, underlining how alienated the commandos had become from the majority of their "brothers".
The Woobie: Etain pulls this off surprisingly well. Right up until she dies trying to save clones who would have killed her had she realized what was going on. Actually, all of the clone troopers pull this off to some degree, especially Atin, who blames himself for his squads' death. He's the only survivor of his squad TWICE.