Complete Monster: Rhade. Where do you even begin with this guy? All the other villains in the story claim to do their deeds for the good of the kingdom/empire. But this guy does all he does because he can. From the first moment Magnus meets him, even though they're on the same side he condescends him constantly, despite Magnus having saved his life earlier (Rhade actually complained about Magnus not being fast enough), and then kills an unarmed old man as soon as he leaves the room. Then he punches you out when you try to defend a rebel leader which begins the downfall of Yumil as Rhade's the one who shows him only power can change things. THEN he forces slaves from the west to be drafted into the war by holding their own families hostage, and saying that it's YOUR fault for dragging them into the war! Quite frankly, it feels awesome when you finally get to stick a sword in his gullet (Or see it, depending on your alignment).
Game Breaker: The Item Duplication Glitch. It's a method that allows you to create up to 99 of any usable item. To which you can duplicate stat upgrade items, alignment upgrade items, even Champion Statuettes!
Ho Yay: Any scene featuring Yumil and Magnus is full of this. Like Yumil asking Magnus to "become his knight".
Grapplers, as they hit hard no matter where in the formation they are, and always come in groups of 3 or 4. Thankfully you only face them in a few levels and you can get one.
Faeries and Gremlins, as they're Fragile Speedster incarnate and will dodge your attacks half the time. They only get real bad when paired with a healer at least.
"Harassment Specialist" units tend to be this way: squads containing lots of status and debuff-casters like the above-mentioned gremlins, fairies and also witches. They're typically not dangerous in terms of damage but since they can put your soldiers to sleep, paralyze them or just decrease their attack power, they can often hold off superior forces (and when you consider that 'losing' a battle, even on technicality causes your unit to retreat back a ways, it can cause a lot of issues).
Cockatrices can petrify you and the cure for that is not cheap. Also, on your side it robs you of experience as petrified enemies don't give any. At least you can upgrade your Golems into Stone Golems thanks to them.
Magnificent Bastard: The Glendale brothers, but Baldwin tends to be more bastard and Richard is more magnificent.
Scrappy Mechanic: Chaos Frame and alignment, two linked traits. While CF is supposed to demonstrate the difference between responsible and vicious tactics, it's so obscure that virtually all players fail to realize the difference between "capturing" a town and "liberating" it is anything more than flavor text. Alignment, while actual visible to the player is absurdly difficult to control in any meaningful as well.
Strawman Has a Point: A number of characters, even Rhade despite his Jerkass personality, bring up that rebelling against the puppet government in Palatinis will only bring about war with Lodis, which they argue is hopeless. Much as the player would hate to admit it, since this is also brought up by someone from the rebellion that sides with characters using demons, they have a point and no matter what ending you get, there's mention that will be a war with Lodis.