At the end of the Scholia Arcana questline, the Dark Empyrean will still be at the same level she was at when you first encountered her in the questline's first quest, whereas you've more than likely leveled up several times since then.
Demonic Spiders: Thresh can be quite problematic for low level players and even mid leveled ones depending on their equipment. They are strong, prefers to keep their distance and almost always come with a pack of Boggarts.
Crudoks are met fairly early in the game and can be quite a challenge for the poorly equipped. They are swift for something of their size, have a very annoying ranged attack that homes and a strong poison attack on melee range.
Ettins can become a problem especially when fought in groups, they are hard to knock, have annoying attacks and can stunlock the player easily. The Shaman variant has a shock spell that hurts quite a bit too.
Jottuns on their own are at most a nuisance, however fighting two or three of them becomes a chore since they are almost immune to hitstun, their attacks cannot be parried and they hit quite hard for a semi-common enemy.
Bolgans offer a similar problem to Jottuns, however they also bring a shield making them more difficult to deal with, especially if you have something else pestering you during the fight.
Niskaru Hunters/Bloodhunters. These things are very fast, can cause bleeding (which decreases defense and saps HP like poison) and can hit pretty hard too. To make things worse they never come alone and sometimes they serve as backup for bosses.
The Mage type of enemy can be deadly when they come in groups. Between throwing homing tornadoes and bombarding you with firebolts, they can also create a shield to protect them from ranged attacks and they teleport if they start to get hit too often. Archmages are even worse as they have a potent ice spell, though it takes a while to charge, that will make the life of any Might based character hell slowing them down to a crawl if the spell connects.
Trolls. Hulking and very strong enemies that are also quite fast when they decide to chase you if you are pelting them with arrows and spells. Trolls can withstand a lot of punishment and their attacks hurts a lot, especially in Finesse and Sorcery characters, to make things harder they have very high elemental resistance turning elemental weapons into a liability. Prismere Trolls are buffed up Trolls and take their most deadly qualities up to a notch.
Designated Hero / Designated Villain: The principal players of the House of Ballads tale are in-universe examples. The Maid is sick and tired of her role as a villainous loser, while the "heroes" this time around ultimately don't live up to their roles. King Wencen reveals himself to be a Dirty Coward when he realizes the Maid could actually win this time and tells you "Here. You're King Wencen now." before running for the hills.
The mage's Meteor spell can instant kill everything in a large area that isn't highly resistant to fire. That pretty much means everything but trolls and Niskaru Lords become laughably easy. Its main weakness is the fact that it has the longest cooldown in the game...which is still only thirty seconds, so by the time you run to the next group, it's ready again.
The game has a potential equipment effect that reduces casting cost, but the internal calculation is wonky. Not only does the effect reduce the cost by a flat percentage rate, not a proportion -at one hundred percent reduction, spells are free- but it stacks multiplicatively, so you really only need about 85%, or so. This isn't hard to get,note You can get 40% reduction from two rings you'll earn as part of the Scholia Arcana questline, another 20% from the higher-level Sorcery destiny perks, another 20% with but ten points invested in Sorcery, and a final necessary 10% from a purple helmet you can find in the first area after the tutorial. and since high-level magic is balanced by casting cost, not recharge time, (all of which are relatively negligible.) you can use all of your gear to upgrade your health and armor, instead. It's almost impossible to lose at this point.
As with most newer Western RPGs, liberal use of crafting, namely blacksmithing, takes any semblance of difficulty and pounds it into oblivion. Maxing out Black Smiting can be done hilariously early, especially if one chooses a race that gets a bonus to it. Load up on health and mana regenerating components/gems, grab the crappiest weapon and armor of the highest type you have access too, save scum a little to make sure you get the base crafting item out of them, mix it all together and you are wearing clothes and wielding swords that are twice as potent as even the strongest items you could possibly have access too, at less than a tenth of the cost of actually buying a piece of gear that would laughably be called comparable, and allowing you to sell the immensely valuable gear you'd normally want to wear. Enjoy virtually unlimited gold, health and mana.
By using the diplomacy quest in The Legend of Dead Kel to trade with Emberdeep for flawless blacksmithing components it becomes pathetically easy (if somewhat tedious) to craft a set of armor that makes you completely invulnerable while at the same time providing an insane damage bonus. There is no difficulty to be found anywhere after that.
Also "Reckoning mode" is essentially an "I win" button. It slows time and boosts your damage output to ludicrous levels, making any fight in the game laughably easy.
There's the scattershot ability, which when combined with other longbow abilities, all bleeding related abilities and the right armor can deal thousands of damage total, is more or less guaranteed to cause bleeding and potentially poisons the target too. Also, you can make poison propagate to other enemies and bleeding can randomly deal a lot of bonus damage. With this setup even the normally rather weak shadow strike ability which is supposed to enhance your attacks rather than actually dealing significant damage, can oneshot a prismere troll.
You can kill a Jottun with basic stealth. Or an entire army of them. Or kobolds, or anything else for that matter if it isn't a troll or niskaru. In fact, with the smokebomb ability you can backstab most humanoid bosses, killing them in a single hit. This is particularly funny if you have this ability in the Scholia Arcana quest line, you can kill the same boss up to four times with it. A boss so incredibly powerful that the most powerful mages of their time only managed to seal it away. Presumably none of them had thought to use a dagger.
Most enemies have a weapon type that just erases them from existence. Chakrams are useful against giant-type enemies, and Squishy Wizards go down with a few greatsword hits.
The jack of all trades builds, while normally somewhat underpowered, have potentially the most raw power out of any build. It's the path with by far the most possible ability choices, which enhanced with a +4 to all abilities can potentially have every possible ability up to tier 4 maxed or close to it, making it the second or third best path for everything and giving it all possible basic attacks allowing the player to tailor their offense to the target's weaknesses, as well as letting them spam attacks almost indefinitely making it impossible for most enemies to even try to fight back. The only real downside is that it doesn't get the most powerful abilities of more specialized builds.
Goddamned Bats: Wolves especially early in the game. They come in packs and tend to coordinate their attacks to flank you, they also stay just a bit out of your melee weapon's reach and can cause the Bleeding effect which slowly drains your health and decreases your Physical Defense.
Venomspitters are met quite often early in the game, they aren't very dangerous even in groups, but if they land any of their attacks it will poison your character taking a bit of their health and also decrease their physical attack momentarily.
Boggarts are at most a nuisance even at the very beginning, however they can distract or stun you enough for a Thresh to land its dangerous attacks on you. Likewise Brownies serves as this for the much more dangerous Crudok.
Sprites are mostly pests you can quickly dispatch even early in the game, but they normally comes in groups of 3 to 5 and absolutely loves to interrupt your attacks/spells. A group with a Sprite Champion from any element can descent to Demonic Spiders territory if one is not careful.
Arcane Barghests are problematic mostly because they sap your mana if they damage you.
The Infinite Backpacks glitch accessible by the time you reach Mel Senshir. Considering how many items in the game are bugged and cannot be removed from your inventory ever, being able to increase your inventory limit well beyond the 120 (130 with dlc) default maximum is a lifesaver. Granted, by the time you reach Mel Senshir you've likely already gone through most of the game enduring the inventory bugs...
It's Easy, so It Sucks: A common complaint about the game; since the game is so combat-focused, most character builds are ridiculously overpowered, and whatever little challenge the game provides can be mitigated with potion-and-Reckoning abuse, most players can overlevel and breeze through the game before they know they've done so. It doesn't help that you have to actively try in order to avoid the Gamebreakers.
Player Punch: Arguably the House of Sorrows storyline. The person that originally inducts you into the House of Sorrows uses you as a means to destroy it from within. Basically everyone is dead and the Second Coming of the House's founder has to sacrifice themselves to save the world. Especially punch-worthy as the Fateless One would be coming down from the hight of recently breaking the Mel Senshir siege and that was one of the reasons the player is approached to join.
That One Boss: Mage type bosses like the Maid of Windemere, the Dark Empyrean, and Templar Octienne can be fairly challenging given their variety of powerful elemental ranged attacks, teleportation abilities, and constant summoning of mooks. Especially jarring given the relative ease of the game. Reckoning does make them considerably easier, but if you don't have a full Fate bar or a Fate potion ready, death is a real possibility.
Also extends to Boss in Mook Clothing like Bog Threshes or Crudoks. Groups of Sprite Champions can also be a real handful if you're not prepared to instantly take them out. Sprites can use weaker variants of the Sprite Champion, Champions can use other Champion's attacks as well. For mages this is particularly hard as Sprites get elemental resistance from their Champions, and most of a mages' weapons and offensive abilities deal elemental damage. For the same reason Trolls tend to be tough fights for mages, they have very high elemental resistances.
That One Side Quest: "The Guiding Hands" can become this if you haven't been leveling your Stealth skill up to that point.
"The Killing Ground". You need to escort a suicidal warrior with pitiful health and defenses through hordes of Tuatha and Prismere Trolls.
"Long Overdue" isn't hard as much as it is really annoying. You get it in the first town in the game, but it can't actually be completed until almost the end of the game. And the reward is a measly (and especially measly for the point of the game that you'll be able to complete the quest) amount of coin.
To elaborate: as many quest items in the game cannot be removed from the inventory (such as put in your stash), you end up going through THE ENTIRE GAME with all the books you've collected taking up precious inventory slots. Which is likely already bogged down with various other bugged unremovable items for all the quests you've already FINISHED. Of course this can be avoided by simply ignoring the books until you can access them all, but by the time you're aware of this you'll likely already have a few under your belt.