The way this game handles making choices is actually brilliant in hindsight; you're not just making a choice, you're deciding between which of Jin and Cassius' courses of action you wish for Dust to take.
The residents of underground city of Mudpot speak with a southern American accent. It's easy to pass this off as a style choice until you realize that the game refers to the four cardinal directions by how they relate to the world map (left of the screen is west, right is east, etc).
During the war sequence- no matter how vicious his fighting gets- Dust never strikes allied NPCs. However, this is also an example of Gameplay and Story Integration: Ahrah is a compassionate being, and (if Dust's ability to jump higher while attacking a target is any indication) is directing Dust's attacks to some extent. Of course he wouldn't attack allies!
It may also have something to do with how the Cassius part of Dust is an incredibly skilled fighter - he's good enough to just not hit allies.
However, if Dust AIR GRAPPLES A FUCKING AIRSHIP, the explosion will hurt both friend and foe alike...which makes sense, given that it's pretty much impossible to aim an explosion away from someone in the blast radius without a shield of some sort, and Dust can't do that.
Why does the evil presence in the box attach itself to Dust instead of Fidget, when she's the one who opened the box, not him? Because Dust's twinned souls make him demonbait, so of course it'd go for the tasty one.
In order to be able to buy forge-able materials in the shops, you have to take the material from a monster you killed, then sell it to a merchant. This is fine and all, until you realize that one of these items is a Dog Tag. How the merchant gets his hands on these can only be left to the imagination.
At the time Dog Tags becomes an available resource the war between the Moonbloods and Gaius' army is in full swing. It's not entirely unreasonable to expect that Moonblood soldiers sell or give looted dog tags to the merchant.
Going back to older cutscenes after The Reveal, realising that Ahrah has been lying to Dust literally from the minute he came into the world as a conscious entity, gave him a name based on what he is, and has been manipulating him the whole game to assure that he's a suitable Laser Guided Tyke Bomb to take out Gaius. And these are the good guys.
The Moonbloods are the good guys? Says who? While Gaius is certainly taking extreme action, he seems like a pretty reasonable fellow all told, and if you think about it, the Moonbloods brainwashed Cassius into doing their dirty work for them. If such mind control has been done previously, it is no wonder that General Gaius and the King wanted to wipe them out.
The Moonbloods didn't exactly "brainwash" Cassius (even though Gaius believes this to be the case), since both Cassius and Jin were already dead, or, at least, mortally wounded, having slain each other in a way that created a bond between their spirits, allowing them to be combined into Dust. This is why, during The Reveal, Dust seems to have regained memories of both. It's worth pointing out, though, that even Dust himself gets fed up with Ahrah's cryptic "guidance" on at least one occasion. Then again, since we never see the full extent of the abilities the Moonbloods possess, it's entirely possible that there have been cases of them doing something even more morally questionable: perhaps those who started the genocide knew something about them that we never find out.
According to Elder Gray-Eyes, everything Dust did was (somehow) Just as Planned. Including killing Fuse. Coincidentally, Elder Gray-Eyes is also the one who, to save his life, gave Fuse his magitech prosthetic armor that tragically induced Cybernetics Eat Your Soul and turned him into a rampaging genocidal madman who needed to be put down. Now what about Bopo's father's illness, and the unexplained "darkness" that ALSO turned Lady Tethys into... *drumroll* a cackling, effectively-genocidal madwoman who needed to be beaten with a sword until it magically went away?
I think it's more that Gray-Eyes saw what was already happening, and planned for Jin's compassion to rectify both situations. With Fuse, he may have seen Fuse slipping into genocidal hate, and subtly sent Dust after him, as well as sending making it so that Dust would stumble upon Mudpot. I don't think he directly planned for the surrounding events, so much as, at best, saw them, and planned for the Sen-Mitrarin to fix them by subtly sending him those directions
Even while amnesiac and stifled by/conflicting with Jin's soul, Cassius is enough of a badass to trek across half of Falana and almost singlehandedly kill every predator and enemy soldier- including actual magical beings, mind you- that gets in his way. This while he doesn't even remember (consciously, anyway) whatever military training he got before turning into Dust. How many Moonbloods must this guy have slaughtered when he had full command of his memories, bloodlust, combat experience, and a national-scale army backing him up?