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.
Alternate Character Interpretation: For just about anything in the planet, being that neither you nor the characters ever find out why everything is so hostile even if minutes ago, or in the Children's case just moments, they were peaceful with each other. Providence in particular, being the one that caused the crash in the first place, stands out. Is he truly the Bulwark of the Weak as his title says, merely defending the planet's life from what he perceives a hostile force that is carving a swath of destruction in its way? A warrior whose plan to find a proper challenge went terribly astray at the cost of life that finds itself hostile to humanity? Amurderer that brings down a ship and kills almost all the crew, and then commands peaceful planetlife into attacking you against its will to clean up what's left? What goals does he have, ifany? It's hard to know.
"Coalescence", the theme of the final level. A combination of haunting and general badassery, fitting the tone of the level itself and instantly conveying a sense of finally returning to where it all began. The name of the track is very fitting—it sounds just like an emotional finality of everything you've been through, all that hell, coming together into a climactic coalescence.
The actual boss fight gets Precipitation, which is simply badass, with a touch of otherworldliness that fits Providence quite well.
"Monsoon", a song that plays in one of the first levels, has an excellent blend of sci-fi and mystery, making for a great first level piece.
Demonic Spiders: The enemies that shoot the red rockets that do massive damage to you. They become extra stupid for close-combat classes because they can then hit you with them point-blank, leaving you to wonder why you just lost 50% of your health from what would've been a barrage of rockets.
The red Clay Men in particular are utterly nasty, due to already being horribly fast, being accompanied by the tougher variations of themselves to soak up your shots, and slicing you up for even more damage.
Game Breaker: If you manage to spawn in a variant of the third level that includes the Easter Egg area with endlessly respawning Toxic Beasts, you can essentially keep killing them with no risk even with melee characters if you position yourself correctly, allowing you to both collect a seemingly endless supply of items as well as use the smaller boars they summon to max out your base health at 9999 with the Infusion item, the combined effect of both of them being enough to withstand basically almost any kind of enemy swarm from even the highest combined base and Dynamic Difficulty possible. Then again, considering how much of an ass the RNG can be when it comes to getting essential items, you need all the help you can get, especially with the game's spotty multiplayer functionality and because the game expects you to beat it at least 5 times to unlock the last playable character, which is not an easy thing to do even on the easiest base difficulty.
Certain combinations of the artifacts are this. One of the most notable is a combination of Glass and Command. Glass causes you to deal 500% damage, but you only have 10% of your maximum health. However, Command allows you to actually pick which items you get from chests and shrines, meaning that, if you're lucky enough, you can get an Infusion as early as the first level. Combine that with all of the free useful items that you're going to be getting, and the game becomes a breeze due to the fact that Infusion all but completely negates the fact that you have a very, very small health bar.
Wanna break it even further? Pick, alongside Glass and Command, the Kin and Honor artifacts. At first glance it seems like you'll be only making your experience harder, since it'll lock the enemy spawns to a single species per map, and the RNG can still screw you royally just the same if it picks an species hard to apply crowd-control, and the Honor Artifact will ensue every single spawned enemy is an elite, harder to kill version than their normal counterparts... Until you realize that as soon as you find a green-rarity chest and choose a 56-Leaf Clover, which gives every killed elite enemy a chance to drop even more chests (an effect which you can stack up to six more copies of the artifact if you feel inclined to maximize the bonus), you will be able to farm for as much equipment as you can dream about in the first stage with minimal luck as long as you don't activate the exit teleporter. Added with the fact that with only one species to assault your survivor, minimizing sneak attacks and boosting survivability odds, what's there to fear about time-increasing difficult when you can come out decked as a God from the very first stage?
Goddamned Boss: The Cremator. His only attack is reasonably easy to avoid, as it's telegraphed and you're Crosshair Aware of where it's gonna land, but it spawns all the way down in the magma pits in a stage where the teleporter is usually at the very top, can hit you from anywhere in the map, is fought in an arena made of small platforms with lava that hurts quite a bit, and he's got a turtle shell that blocks attacks that aren't from the front, which combined with the stage and its swimming makes it invulnerable half the time. Melee characters will have hell trying to bring it down in any reasonable amount of time. In any other game, this would be just annoying. Here, it could well mean that You Are Already Dead due to the increasing difficulty.
The Wandering Vagrants on the final level. They spawn in packs and have too much collective health. Sure they can't hurt you if you keep walking, but since they're blocking your shots and just generally being in the way for several minutes at a time that's not much consolation.
Nightmare Fuel: If you think about it, there's a surprising amount for a game with a minimalist style story. You're trapped all alone on an unknown planet full of monsters and aliens that should be docile, but for some reason go into homicidal fury whenever they see you. The "upgrades" that are essential to your survival are, with few exceptions, essentially mutations, ranging from the mundane (fungus on your head that heals you), to outright Body Horror (replacing your own eye with the eye of the Magma Worm, cutting yourself with a cultist knife, etc). If you read the monster logs from start to finish, it becomes clear that the survivor is slowly but surely breaking down as a result of the hell they go through, and the ending all but confirms this.
Squick: A syringe, named the "Soldier's Syringe" is filled with a lot of stuff, both understandable for its use, and some other questionables. Right from steroids to gasoline. Even the sender of the item says it got a few of his soldiers killed (and the rest sick from overdosing), but otherwise works.
That One Boss: Most of them, actually. Though, the Magma Worm tends to stand out. It can spawn on the first two levels, is one of the few bosses capable of following you across the entire level, and it gets faster (if less accurate) the closer it is to dying. Naturally, it is the bane of many an early run.
Late runs too when you revisit levels and have bosses spawning randomly. You can run from almost any other boss and the ones that attack globally generally are still easily to avoid, but Magma Worms stand out in their ability to chase you constantly with attacks that are more difficult to dodge than "avoid this crosshair". A pack of 2 or 3 of them can cause issues for even end game characters.