These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Several (this being a roguelike, after all), but a special mention goes to the Octos, who occasionally decide to spam painful aethereal bolts at you while you're running away.
Eelys are these early game. They show up in bodies of water and almost alwatys a reasonable distance away from you when you enter their room. They spit powerful acid bolts which can end your run depressingly quick.
Even worse are enemies and traps that can Corrupt your equipment, reducing their bonus to the point of being detrimental to your stats. Special mention should be given to Diggle Archmages, who can Corrupt your equipments at range (others Corrupt at melee range and can be kited around). Make sure to have 100% Magic Reflection when you face them.
Obvious Beta: Upon release, Conquest of the Wizardlands had more bugs than the rest of the game put together.
According to the Gaslamp Games forums, the Egyptian Magic skill is this, to the point where it's been nerfed by a patch almost immediately after it came out. It still is incredibly powerful though. Thus, some people reported cleaning level 15 zoos with ease.
Necromancy is meant to have great effects balanced by debuffs and damage after casting... except the damage can be prevented by just a few points of necromancy resistance, and the last three levels of the skill GRANT necromancy resist and have disproportionately small costs for their effect. The fourth skill on a good tank build allows you to survive in melee combat indefinitely and costs next to nothing, and the last skill does huge damage over time to a huge area that'll take out most groups of monsters in one shot in exchange for a few dozen turns of marginally weaker magic.
Game-Breaking Bug: Murderous Rutabagas and their sprite-swapped counterparts used to charge at you several times in succession and give you so many stacks of the Food Poisoning debuff your maximum HP would go low enough for you to die in one hit, which they'd gladly deliver. Fortunately, this was just a bug, which was later fixed.
Goddamn Bats: Pumpkinns and Witchies can be annoying depending on your setup. Pumpkinns have a high attack and can summon an Area-of-Effect gas over you that, even if it doesn't hurt, it will still drain any buffs that have a hit counter by at least 2. Witchies can blind you if they choose and you don't have high magic resistance, as well as bring back the dead. That being said, neither are too deadly on their own even if you don't have a counter for them.