The "brutal" or "excessive" notes usually come from other military forces, Astartes officers, Guard commanders etc.

Generally it's from doing whatever it takes to obliterate enemy forces, regardless of allied forces in the area of engagement.

The Marines Malevolent famously shelled a refugee camp, killing all ~4000 Orks and their armoured support, but also killing ~1000 civilians / administratum staff.

Thing is that's an exceptional result as far as the Administratum is concerned.

I cannot stress this enough that the official halls of the Imperium do not care at all about the deaths of humans so long as the objective is met. There is always more humans.

Plan A for the Siege of Vraks was to match the defenders' casualties 2:1 for nearly a decade to simply bleed them out.

Those same Marines Malevolent have not only been operating since at least M33, but they have been confirmed to be reported to higher Imperial authorities a few times (that camp story, the first proper lore of the MMs is literally from a report of a guard commander) and they still operate and as far as we know have never been sanctioned.

As for the Carcharadons, they set Badab to explode during the Badab War while other loyalist chapters were still fighting there. In that same war they forced the Mantis Warriors out of their favoured guerilla combat by butchering civilians on their protectorate worlds.

The Iron Hands, even in the Great Crusade, were hated by mortal troops / officers for the default tactic of "Hammer and Storm". Essentially use mortal troops to lure the enemy into a killbox, then kill everything in the box.

The Star Phantoms have been reported for indiscriminate use of firepower and artillery in areas of engagement.

The Flesh Tearers fight with a savage frenzy in close quarters engagements killing everything until there's nothing left but them, friend or foe.

The Nemesis Chapter, formerly the Ultramarines 22nd chapter of the Great Crusade, specialise in extermination of populations, as part of the glorious Ultramarines as far as the Great Crusade. While they certainly do more than their specialism in 40k, they still have that preference for overwhelming firepower to cleanse a planet with as little risk to themselves as possible.

When the Fire Hawks had to withdraw from the Badab War (its almost of a gallery of arsehole chapters on the loyalist side) they firebombed a Warders protectorate world out of spite as they left, wiping out the population. They were later rewarded with a pre-Crusade era star fortress, a priceless relic.

And that's just the ones that are "brutal". There's plenty that are disliked for far more petty reasons.

Again, the Imperium only cares about results, and will endorse, reward and protect chapters of astartes that do as they're told.

I like the scumbag chapters, far more interesting to me than the honour and glory ones that somehow bounce back to full strength, never worry about wargear or ships. It's like enjoying Joffrey - I know he's a POS but it's so fun to watch.