Per wiki policy, Spoilers Off applies here and all spoilers are unmarked. You Have Been Warned.

The ghost girl isn't real

Someone noted the girl targets the most paranoid worker (the game counts on how many times you turn and looked back) or someone who carries the most valuables. The former reason could imply the girl is actually merely hallucination as no one else could see her and you can't scan her; also explaining why she was always following you and unstoppable. You probably simply died of paranoia, it's all in your head.
- At first only one worker had paranoia and seeing her. But once that worker died other worker started to get paranoid and believe there's ghost as well, so it is spread.
Someone else suggest there is hidden sanity meter but this is not proven.
The ghost girl explodes you into bloody gore visible to everyone. That ain't paranoia.

There will never be a way to repair the tantalizing drill at HQ.

The Ghost Girl is a child from a 'higher dimension'

She's just playing with what would be the equivalent of tiny insects to her: completely defenseless and unable to communicate back. Just like an ant that's being poked by a human, the victim won't be able to perceive the human's finger until it gets too close, which is why only the Ghost Girl's targets can see her. She's playing with you, and only you, until you get squished and she decides to keep playing.

A new monster in the future will be a nod to The Upturned.

If you've played to the end of the game, it's mentioned that before the world got destroyed by a meteor, amalgamations of irradiated boars called "Outsiders" ambushed people in their sleep and dragged them away, never to be seen again. The likes of those would snugly fit into Lethal Company.

Jesters, Nutcrackers, and Coil Heads all come from the same manufacturer

These things are ostensibly metal toys and figurines intertwined with biological parts and functions, with Nutcrackers having a biological eye and presumably other organs in its chassis given the amount of blood that bursts out on death, Coil Heads being theorized to be bioweapons, and Jesters being full of flesh and bone, with all three of these things having a predatory instinct to chase and kill anyone who enters their territory. They might have a common origin of all being created by the same manufacturer who intended them to be bioweapons and security measures meant to protect the buildings they inhabit, or are just a series of batshit insane inventions made by the same group of madmen.

The workers aren't human

They never take the suits off, and nothing can be seen behind their visors.
They don't seem to eat, drink, or blink, and a fully intact worker corpse weighs 11lbs.
The only other thing we see employed by the Company is a tentacle monster operating the company store, so it's not a stretch to imagine that other nonhuman creatures are working for the Company as well.

The workers don't even get oxygen tanks

The tanks the workers universally carry on their backs are commonly assumed to be oxygen, but the workers clearly don't have any independent air supply since they can't survive underwater. In fact the only thing their suits seem to protect them from at all is the Spore Lizard's defensive spore cloud, but who knows if that's even harmful in the first place?
The orientation clipboard notes that the worker's hazmat suit helmets are equipped with the advanced echo scanner, a device seemingly a cut above every other equipment item they have, until you read the fine print and realize the scanner earpieces on the left and right side of their heads constantly release ionizing radiation.
The hoses from the tanks aren't plugged into the breathing apparatus at the front, but rather into the earpieces. Therefore the tanks probably aren't even oxygen, just some kind of fuel or catalyst for the scanner. The company just forces employees to use regular gas masks with dangerous built-in scanning devices that require them to lug around tanks full of some possibly-radioactive gas.

The Masks are made of blood and/or bones

The Masked turn workers into more Masked by vomiting a bloody substance onto their face, implying that the stuff creates another mask on the victim. The masks are white, though, meaning that it could be a host's crushed bones that make up its composition. Alternatively, the shiny semi-metallic look means the mask is created partially from the iron in the blood.

Alternatively, the mask is a parasitic organism and not supernatural at all

They use mimicry to appear like a Comedy/Tragedy mask and lie dormant until body heat awakens them, allowing them to parasitize the victim and take over their nervous system. Once active, it will use its body to try to find more hosts, immobilize them, and then shoot cells out from its reproductive organ (which looks like the mouth of the mask), which takes the form of a blood spray. These cells quickly form into another mask on the victim's face, parasitizing them as well. The red glowing eyes are likely bioluminescent part of the organism's body, which are normally retracted and only show whenever the mask awakens or reproduces.

The Butler is actually wasps in a humanoid suit and they attack in order to reproduce

Their method of reproduction requires killing a human and then infesting their body to make into a new skin suit/hive. The knife is there to create stab wounds for the hornets to enter more easily, since employees tend to wear masks and protective suits to cover all their orifices.

Meta: Old Birds are inspired by Daleks

These monstrous robots are attacking anything that isn't them, come equipped with a multitude of weapons, one of their hands looks like a whisk, they have a single eye that acts as a flashlight, they can fly and even shout out garbled messages as psychological attack that is worthy replacement of "EX-TER-MIN-NATE! ". Not only that, but one of the hidden planets is a condemned testing grounds of them, not too dissimilar to Dalek Asylum planet.

WMG / Lethal Company