During one test GLaDOS mentions that she has been 'enhancing the truth', and that she will stop enhancing the truth in '3... 2...' and is about to say '1', except there's a sudden burst of static. At first glance it seems like just a hint that whatever AI is talking to you, it's a bit glitchy. But consider this: GLaDOS never finished the countdown, therefore she never stopped lying to you
Why are the only birds seen in Aperture crows, despite the facility becoming more open to the elements in the sequel? It's symbolism; crows are seen as a symbol of death, which is exactly what Aperture is. A death trap.
Besides the thing that GLaDOS is usually attached to, what caused Wheatley to become Drunk with Power in the first place? Remember that GLaDOS claims that Wheatley was specifically designed to be a moron. Which means to make the worst decisions possible, he has to know which is the best decision in any situation and do the exact opposite of that decision. Its specifically part of his programming to choose the worst decision he could do in any situation. Possibly another reason why Wheatley became Drunk with Power seemingly out of nowhere is because letting the power go to his head is the worst decision he could make in the situation. In that situation, he was just following his programming!
Cave Johnson's backstory released in supplementary materials before Portal 2 is contradicted by what we know from playing Portal 2. Is this a continuity error? No! Turns out, as of the Perpetual Testing Initiative, that there is an infinite multiverse filled with an infinite number of slightly-different versions of Cave Johnson. We were just reading the backstory of the wrong one. This can also explain why all of Aperture looked and functioned differently from Portal 1 to Portal 2 (aside from the meta explanation of design changes between games.)
Wheatley isn't stupid, he just does things in the most destructive, round about, insane, bumbling way possible. He just wanted to leave the facility and free Chell and he did leave the facility and free Chell. This explains his moments of brilliance, making him an accidental Chess Master. Additionally, why would he be a Chess Master when he was designed to be stupid? Everyone at Aperture science is a complete idiot. Of course they'd cock even that up!
Why do Wheatley's tests all have bottomless pits? On a second play through you may notice that the Docking Station Wheatley fails to find is 500 feet beneath you. He won't or can't come down when you fall in the hole and when he detaches himself from the Management Rail he is afraid to let himself fall the 6-8 feet to the ground, and he yells and screams whenever he accidentally looks down into a dark chasm. Wheatley is afraid of heights, so naturally he sees them as an ultimate challenge in tests.
At one point when Wheatley is trying to "hack" the neurotoxin generator, he starts talking to it in an effort to bluff it into submission. ("Hello, I am the neurotoxin inspector, from the... ah... International Board of... Neurotoxin Inspectors.") This can be taken as just Wheatley being an idiot as per usual, but then you realise: this is Aperture Science, which gives artificial intelligence to everything. Additionally, Wheatley seems to have issues with telling the difference between non-sentient machines and AI's like him. He shouts at the clearly automated Announcer to "SHUT UP" and said he allowed it to "Keep his job." He also says that football is cruel because it's about "Kicking a ball around, for fun."
How the heck did GLaDOS have enough robots to set them up as the ending chorus in the short amount of time she had? She likely took all of them from the screaming robots room.
Alternatively, they were all in storage, in boxes. Seeing Wheatley wasn't smart enough to realize they were in storage, he inadvertently sent the wrong ones to ambush Chell earlier. So, it shouldn't be too hard for Gla DOS to unpack all of them already in storage. As for where she got the "fat turret" and the "king turret", it could be possible that they were prototypes that were also in storage.
It seems strange that, in Portal 2, Wheatley seems to come much much closer to actually threatening and killing Chell than GLaDOS did. The reason is, his incompetence and lack of managerial expertise leaves him single-mindedly testing, and then later attempting to kill you, at the expense of upkeep and stability. He's literally throwing everything at you, while GLaDOS held back at least enough to try and maintain the place.
It's strange that GLaDOS was able to try to kill you, however passively and uncertainly, before you actually incinerate her morality core in the first game. But then, the core was the only core in both games that was completely silent, in addition to falling off the easiest... meaning GLaDOS was a woman of loose morals. It's also possible the core was forcing her to give you a way out of each of your deathtraps.
On a related note, many assume that the Morality Core may not speak because it's broken/catatonic/dead. But fast-forwarding all the way to the end of Portal 2, Wheatley complains about Chell being "quiet" and "judging [him] silently," the "worst kind". The morality core is silently judging (consider how it looks directly at you while you hold it, unlike any of the other cores.)
Another explanation, going by what she says on the final battle ("It was a morality core they installed after I flooded the Enrichment Center with a deadly neurotoxin, to make me stop flooding the Enrichment Center with a deadly neurotoxin.") is that the Morality Core's only function is to keep her unable to activate the neurotoxin emitter, either because it became corrupted, or just a case of Aperture Science being Aperture Science.
Speaking of GLaDOS' cores, she's noticeably much more emotionally subdued this time around, and the references to cake are far less common. Why? Because the Anger and Cake cores were destroyed along with the morality core.
The Thermal Discouragement Beams can cleanly slice through metal pipes, but take nearly 2 seconds to kill Chell. Why? Aside from Chell clearly recoiling from the beams, human skin is not as good a thermal conductor as metal.
Several of GLaDOS' phrases in the first game came directly from listening to Cave Johnson's speeches accessed through Caroline's memories stored within her.
Cave: "In layman's terms, that's a billion little gizmos that are gonna travel into your bloodstream..."
GLaDOS: "In layman's terms: speedy thing goes in, speedy thing goes out!"
Cave: "Why not marry safe science if you love it so much?"
GLaDOS: "Maybe you should marry that thing if you love it so much."
Cave: "I punch those numbers into my calculator, it makes a happy face."
GLaDOS: "Now these points of data make a beautiful line."
During Evil!Wheatley's"Reason You Suck" Speech you wonder why he constantly brings up all the times he thought he was going to die? Because, as was stated earlier in the game, GLaDOS' body backs up the last 2 minutes of a computer's life before its death, forcing them to relive those moments over and over. Now is it any wonder if Evil!Wheatley was not just into the testing for the "euphoric response"?
How was GLaDOS able to cool down the reactor core so quickly? The BSODs you encounter prior to the final battle imply that all she had to do was press a key.
Aperture Science uses the whole bullet! As evidenced by the investment promo, the inner workings of the Turret are nothing more than spring-based catapults. They're freaking glorified airsoft guns. Which is why you can take more than one bullet despite only wearing a jumpsuit; it doesn't kill me, it just HURTS!
Why did Wheatley decide to go through every potential password to stop GLaDOS, rather than just make a guess? Probably stupidity, but also because he's a computer: Computers solve problems by going through every possible solution until one fits, a brute-force method which usually is very effective in computer code-cracking. The only problem with Wheatley, aside from absentmindedly skipping potential solutions, is that he does it at the speed of a human, which makes it extremely time intensive.
GLaDOS' irritation when Wheatley starts insulting Chell at first comes off as just hypocritical, but she may have other reasons to criticize his insults than to needle him; Wheatley's insulting her wrong:
The first thing Wheatley tries to do is call Chell fat. Cue GLaDOS pointing out, "Look at her, you moron. She's not fat." This is true, but hasn't she been calling Chell fat the whole time? Well... not exactly. She's been calling her heavy. For one thing, muscle is heavier than fat; for another, Chell is wearing new long-fall boots and carrying a stable singularity. GLaDOS might have implied she was fat, but she never outright said it, because it's not actually true.
Not to mention, GLaDOS is a computer who sees everything as numbers in boxes. Factually speaking, the slender, athletic Chell IS heavy... compared to a paperclip, or a pencil, or a dustmite. GLaDOS may just be omitting that one part
"What exactly is wrong with being adopted?" If you pay attention, GLaDOS never actually says that being adopted is the thing that should make Chell feel bad about herself; the insult is in implying that her birth parents didn't love or want her. Wheatley is completely missing the point, and it's annoying her.
There's also the fact that the potato battery she's plugged into literally won't allow her to lie, because it doesn't have enough energy. She can't just say "you're fat" to Chell anymore, because she would be lying.
At the end of Portal, GLaDOS sings: "I'm not even angry..." It seems to be a Blatant Lie given what happened, but on reflection it might not be. Of course she isn't angry - you destroyed her "anger" core.
Anyone worrying Chell will be dying of moonrock poisoning from conversion gel should note Cave's statement that Aperture were also researching whether jumping in and out of portals would allay the effect of the poison. While it sounds stupid and presumably didn't save Cave Johnson, a lot of their weird ideas have yielded results (portals, brain uploading, mantis men) suggesting Aperture can achieve when they put their minds to it and we shouldn't be too quick to dismiss. Basically you can consider that line a Hand Wave establishing Chell will be okay if that is what you want. (This is in addition to the purifying Emancipation Grills and the fact that Chell hasn't been exposed to the dust, just the conversion gel.)
Realistically, it's brilliance and a case of Shown Their Work to an extent. Just as asbestos is only dangerous when particles and dust are inhaled, moon rocks (in this presentation) are likely only harmful in the same manner. Cave specifically says "ground up moon rocks are pure poison." He's right, and we know it for a fact: NASA learned back in the 70s that lunar dust was harmful, capable of causing acute silicosis. (Not "lunar poison," but definitely a bad thing for your long-term health and comfort.) However, as long as people aren't exposed to free-floating dust, moon rocks themselves are harmless. So as a single piece like a rock or held in a gel, moondust won't hurt you; as a breathable dust from, say, grinding a lot of moon rocks into powder, it's extremely bad for you.note Fun fact, it also smells like burnt gunpowder according to Apollo 14's Gene Cernan, whose LEM was heavily contaminated with lunar dust. Cave chalked it up to "lunar poison," but in fact he's dying from silicosis; Chell, on the other hand, will be just fine.
Additionally, there is another possibility that many people may not realize: That Cave was right about moon rocks and dust, but wrong about the conversion gel. Moon rocks are porous material, which means that could be reason why portals work so well with them. However, Cave probably couldn't get a steady supply of moon rocks to create the amount of conversion gel we see in the game (seriously, even crushing them up wouldn't be able to account for what has to be over thousands of gallons of the gel). It could be possible that the scientists, long after the moon rocks were made into dust, realized that it was porous material in general that allowed for portal surfaces to be able to be formed (which also explains why walls throughout Aperture Labs, and not just the testing chambers, are able to allow for portalling). And seeing that those walls were more than likely constructed from concrete (which there are porous type that allows for moisture to pass through after hardening), there's a good chance that the scientists realized much later that concrete would be enough due to the porous material they're made of and replicated a porous material to be used as a conversion gel instead. Best guess, the conversion gel could actually be made out of chalk or another porous material. Keep in mind, when we are first introduced to the conversion gel, the recordings were old, so that means that at the time that Cave made the recording, it was before the change in the formula (or that the scientists told Cave, but due to being sick/insane, he just kept saying that it was made from moon rocks). Before anyone says it's not possible, keep in mind that a lot of things (for example, Coca-Cola) have had formulas/recipes that have evolved from how they originally were.
Wheatley starts showing a surprising skill at underhandedness later in the game- specifically, after he told you he read Machiavelli. Guess he wasn't making that up.
In the early parts of the Turret Factory. Wheatley tells you that little story about the caretaker killing his robot assistants, and you can still hear their replacements screaming, but no one knows why. GLaDOS mentions she built a room "Where the robots scream at you." Guess that's why they're screaming, GLaDOS just wanted a room full of screaming robots.
Additionally the game mentions that GLaDOS was developing new testing mechanics when Chell killed her in the first game, with the Deadly Lasers and Cooperative Testing Initiative being stated examples. There are plenty of mechanics that got Dummied Out from the final game, some of which are functional enough to be used in community maps. Knowing how obsessive GLaDOS is about testing, it's possible those screaming robots were going to be part of a sound-based testing mechanic that never materialized because GLaDOS blew up before she could finish the project.
Remember what GLaDOS tells you about her quick-save feature? About how it forced her to relive her death for years? It could be a reference to a bug in the first game, where if you fall off one of the platforms in the middle of one of the game's auto saves, you'll end up in an endless loop of respawning and dying.
You may have noticed that when you fire a portal just off of one of the aerial faith plate targets, the projectile manages to autocorrect and hit that center of that target, even if there's a large amount of space on either side for the portal to form, meaning the projectile must be able to seek out some sort of Aperture Science technology. When you shoot the portal gun at the moon, it always seeks out one of the later Apollo landings. Aperture Science spent a ton of money to get moon, of which there's only 380 kg brought back from the Apollos. Aperture Science must have sent up one of the faith plate targets to the moon on one of the Apollos, and the portal projectile sought that out when Chell shot the moon.
$60 is not so much a random number as it was the average cost of a console video game at the time of Portal 2 release.
You know when GLaDOS captures you in the obvious trap and transports you in a casing room similar to the first test? The only other thing with you in that room is a toilet seat. Just seems like nothing at first, but then you remember she's about to kill you and she's seen human death before. She gave you a toilet to empty your bowels in before you die.
At the beginning of the game, the announcer mentions that Earth may have been taken over by a sentient cloud or animal king, and the player just shrugs it off as Aperture being weirdly paranoid. However, in the Perpetual Testing Initiative, there are alternate dimensions containing sentient clouds and animal kings. Assuming the DLC is canon, Aperture was being serious with those announcements.
There was one chamber in the Portal 2 where Cave's recordings warn you that the chamber is used to test time travel. Perhaps he was already trying to extend his life far enough for his brain to be uploaded into a computer as he wanted, and what better way than just traveling to a time period where it's possible?
If you finish the second stage of the final fight with only one second to spare until reactor meltdown, you still get full two minutes on the third timer, even though destroying the second timer didn't actually abort the imminent meltdown. Sounds like standard Anti-Frustration Features, right? But remember, this is Aperture Science. They have a timed self-destruct mechanism designed to remove the uncertainty of not knowing the Exact Time to Failure. What if the second timer is also some kind of self-destruct mechanism, an enforcedExact Time to Failure? If the timer says the reactor is going to melt down in three minutes, then it damn better melt down exactly in three minutes, or else!
So, how is Doug Rattmann, a scientist with mental issues, able to survive in a GLaDOS-run Aperture Science? How can he constantly evade her security and surveillance? How was he sane enough to realize the stupidity of giving a mad AI access to neurotoxin, and clever enough to survive the initial purge? Because of his schizophrenia. GLaDOS describes all the cores attached to her as being like a stream of voices in her head. In other words, Doug knows how GLaDOS thinks.
The potato theme strongly suggests where GLaDOS is getting her supply of neurotoxin. A close examination of the awards received by Aperture shows that they were experimenting with potatoes prior to GLaDOS's creation. There's also an overgrown potato somewhere in the lab, which interestingly enough was actually grown by Chell. And, as we all know, potato leaves contain neurotoxins.
A bit of fridge horror, if Chell was not so successful in her potato project as a child, she may not have the threat of neurotoxins over her shoulders at all times. She may even be aware that she is indirectly responsible, though it is unlikely that GLaDOS would know of this connection. How would she know the connection herself? Having connections to Aperture at a young age, its not too far-fetched to believe Chell is very knowledgable in the science field. In fact, a love for science could be a reason she applied as a test subject.
There's been some complaints about the lack of cake in Portal 2. It makes sense, though: at the end of the first game, you destroyed the Information Sphere, which held all of GLaDOS' knowledge about cake. Even if she still remembers it, she isn't fixated on it anymore without the sphere
A meta explanation could be the cutscene after defeating GLaDOS, in which the player is presented with a cake. So technically speaking, we already got our cake
When you put the first core on Wheatley it says "Warning. Core corruption at 50%". After that first one, it goes up by 25%. This seems inconsistent until you realize that Wheatley is the first 25%.
In Portal 2, we learn that Aperture Science had a Portal Gun in the 50s. Why didn't they bother marketing such a world-changing tool? Because AS has always considered the Portal Gun to be a mere testing tool for their other projects they intended to make money off... most of which had a habit of doing exactly what they were meant to do.
Watching the video "You Wouldn't Know", GlaDOS sees Chell as fat (even though she's not), and looking closely, there's a Fish-Eye Lens distortion. Perhaps she thinks Chell is fat because of the distortion.
It is inconsistent that repulsion gel, conversion gel and (to a lesser extent) propulsion gel don't display any of the damaging effects Cave Johnson claims they have when you splash around in it ingame. While it is likely a gameplay concession, it could also be the fact that the gel has been down there for decades and possibly centuries. The gels may have just went bad (remembering that they used to be food items), or decayed in another way (such as mold or being watered down), thus downplaying the worse side effects of the gels.
Alternatively, Chell is only around them for what could be, at the most, a few hours. Cave Johnson was working with them for at least 10 years. It's possibly just like radiation, a little won't do much, but a lot can kill you
In some unused dialogue, Space Sphere gets tired of being in space and wants to return to Earth. Rule of Funny applies of course, but unless we assume that his desire to go to space was part of his corruption, what functional purpose does this serve? Well picture this: GLaDOS has Space Sphere attached to her and either gets fed up of hearing him talk about space or takes on his desires, and travels to space. But who's going to run the facility? Well then Space Sphere gets tired of being in space, and GLaDOS then either gets fed up of hearing him talking about something else or takes on his desires again, and then returns to Earth. It's a fail safe just in case GLaDOS takes Space Sphere's words in the worst way possible.
The BorealisEaster Egg in the condemned facilities can make one wonder why the hell Aperture saw fit to construct a dry dock almost 4,000 meters below ground... until you remember or learn that the Borealis was a test vehicle for a Teleportation experiment that, if successful, would make access to a river or ocean unnecessary. Anyone who's finished playing Episode 2 of Half-Life 2 will know that the experiment was at least partially successful since the Borealis ended up somewhere in the Arctic Circle, which qualifies this decision as one of Aperture's more sensible (or at least less idiotic) ones.
Aperture's entire shtick seems to be 'testing'... but testing what? Technology, sure, but how many tests do these things need to go through when they obviously work fine already? Unless the technology was only one part of it... and what Aperture was REALLY testing was PEOPLE. Think about it, the games prove that a single person (namely Chell) could easily get through even the most complex tests Aperture could design, and they claim to have thousands of people in storage... maybe Aperture's big plan was to save humankind's best and brightest and store them until they'd be needed the most, like in an apocalyptic scenario when the world needs rebuilt. After all, Chell beats every test GLaDOS throws at her in the first game, and her reward? Being put into suspended animation until the second game's events, like god knows how many other people who passed the tests. Even Cave Johnson's ultimate goal towards his death was preserving human minds by copying them onto computers
Wheatley claims he has a 4-part plan to stop Chell from killing him, he outlines each of the 4 steps, but in the final stage of the fight we see he actually had a 5th part of the plan he didn't mention. Was Wheatley actually smart enough to keep something to himself... or did he genuinely not know 4 and 5 were different numbers?
When you incinerate the Companion Cube in the first game, GLaDOS mentions that you did it "faster than any test subject on record", no matter how long you take to do it. This seems like yet another lie to jab at the player, until you read the Portal 2 tie-in comic, Lab Rat, and find out that Doug Rattmann changed the test subject list so that Chell would be the first test subject chosen. So, in a way, GLaDOS wasn't lying about you being the fastest since you're the only one on the record.
The personality cores were probably Aperture's first success at, as Cave Johnson put it, pouring someone's personality and memories into a computer. GLaDOS claims Wheatley was invented to generate bad ideas... but who's to say he wasn't based on an existing person? Maybe even a fired employee?
At the end of the main Co-op story, Atlas and P-Body have to open the vault by gesturing in front of a camera. Why is that the locking mechanism instead of, say, a keyhole? Well, GLaDOS had been saying that the gestures were symptoms of the bots becoming more human-like. That camera was wired to the vault door specifically as a CAPTCHA. They wanted to make it so that only humans could get in.
This video features a look at the portal gun's inner workings, which includes reservoirs for blue and orange dye. From that, it can be inferred that this is what gives the portals their distinctive colors. So when Atlas and P-body needed to be given guns that shoot portals coordinated to their own colors, modifying them for that was as easy as just changing the dye.
In the end of the game, GLaDOS refers to Chell as a "dangerous, mute lunatic." Many may just assume that she was just calling Chell crazy, but most people nowadays fail to get that the origin of the word "lunatic" was that it was meant to be a kind of insanity supposedly dependent on the phases of the moon. Considering what Chell did previously, GLaDOS was right to call Chell a lunatic, because only Chell would have been crazy enough to open a portal on the moon.
If you pay attention after the "moon shot", you'll realize that one of the items first pulled out through the hole is the very portal gun you have been using. It happens so quick, you may fail to realize it's happening.
Given that we learn GLaDOS' AI was based on a real person, one has to wonder about the cores that were incinerated in the first game and whether they too once started as people...
Remember how Cave Johnson introduces himself in the 70s-era recording? "You might remember me from the 1968 Senate committee hearings on missing astronauts." Aperture Science accidentally killed some of NASA's finest during testing and then tried to cover it up.
Later on, GLaDOS tries to shut down Wheatley by reciting a paradox. Note that, after she does this, Wheatley is unaffected, but the Frankenturrets stop moving, and start sparking. They're sentient, and GLaDOS just killed them. Whoops.
With the implication about the Frankenturrets being sentient, there's the fact that they often head for the Emancipation Grill, if available, and it kills them. So if they aren't just moving mindlessly towards a bright light like insects, are they trying to kill themselves?
As you're on the elevator finally leaving Aperture at the end, You encounter turrets. However, they don't shoot you. Instead, they serenade you. It's sweet in context, but what was one of the things GLaDOS said as she was letting you go? " Don't come back" Those turrets aren't there to shoot Chell on her way out... they're in place to shoot her if she tries to come back in. Depending on when GLaDOS set those turrets up, they also could have killed Chell if she and Wheatley had gone through with their original escape plan.
Potato GLaDOS arguably experiences an in-game occurrence of Fridge Horror.
Potato GLaDOS: Caroline... Caroline, Caroline... Why do I know that name? Did I kill her? Or... Oh my god. Look, you're... doing a great job. Can you handle things for yourself for a while? I need to think.
Somewhat more minor example. One of the warnings GLaDOS gives you when you first pick up the portal gun is to never submerge it in liquid, even partially. Later, it is revealed that the portal gun started as some sort of shower curtain project. One had better hope that the water thing was a lie.
Wheatley was originally designed solely to produce bad ideas, just to give them to GLaDOS. When that didn't work, what do they do with him? They put him in charge of the safety and welfare of thousands of people. Or at the very least, some of the AIs might have done it, which puts in perspective how little they care about the humans in the facility.
GLaDOS at one point says "The companion cube will never threaten to stab you, and in fact, cannot speak." Got a laugh from that the first time, right? Until you realize Rattman was schizophrenic and paranoid, and may have actually experienced those things from the companion cube.
GLaDOS apparently has a backup file of you that should you die she can resurrect you from, in the final battle she deletes it. Who's to say the Rattmann isn't just one of your earlier tries? And all those times you were crushed or fell into acid? Those actually happened, you just don't remember it.
Remember that second time you woke up from your Human Popsicle? The computer dutifully reports that you've been under for "Nine-nine-nine-nine-nine" before pausing and repeating. If the computer isn't broken, that means Chell might have literally exceeded the amount of digits the computer can hold, meaning at least a good 274 years could'' have gone by, if not more depending on how many nines you interpret the machine to be saying and how trustworthy you find Aperture technology to be in keeping time.
When you pass by the children's science fair projects, Wheately mentions "Bring Your Daughter to Work Day ... that did not end well." Then a few minutes later, you realize - the scientist's daycare center is only one door and a few hundred feet away from the neurotoxin generator room. The game never outright says it, but it's easy to deduce that the first instance of GLaDOS flooding the center with neurotoxin lead to a lot of children's deaths.
Wheats and Space aren't the only cores trapped in space...if you watch the cutscene where Wheatley is knocked into space carefully, you'll see the core on the left side of him was also sucked quietly into space like the portal gun: Rick the Adventure Sphere! Whether or not this was intentional on his part or an accident, it's still a bit sad to know that Rick is in space too, without any attention drawn to it at all.
In the Co-op trailer, GLaDOS claims that the cooperative test chambers have "never been solved by a human." Look at what she said. A human. Not "humans". She never bothered sending two humans into the co-op chambers, probably specifically so she could be smug about it.
Wheatley's apology at the end is made a lot sadder when you realize there's no way that he could know that Chell survived and was simply given her freedom at the end. For all he knows, she could be dead.
Notice how the central plot across both games tends to revolve around conflict between sanity and psychosis in a sterile, isolated environment? Play through the first game, and note the padded interiors of the elevators.
GLaDOS giving Chell the Companion Cube at the end seems like a Pet the Dog moment for her, but it's actually one final Stealth Insult directed towards Chell. GLaDOS is suggesting that it's the only companionship Chell will ever get, either because she's a "bitter, unlikable loner" or because she won't find any other humans.
Before the first chamber with the blue gel, Cave Johnson's recording mentions a hapless control group member who ended up breaking "every bone in his legs". Some time later, on another of Cave's recordings he casually mentions firing a wheelchair-bound employee because "ramps are expensive". Narratively speaking, it's a very suspicious coincidence.
The fact that the achievement for incinerating the Companion Cube is called "Fratricide".
Wheatly's fate might not be as permanent as the audience is led to believe - Wheatly was sucked out of a portal into space, but he needs to go much faster than that if he wants to escape Earth's gravity well. This leaves three possibilities:
His orbit decays until he eventually enters Earth's atmosphere and likely burn up on re-entry - if he still has power to function by then, it's not going to be a nice death.
He collides with one Earth's many satellites, natural or artificial - likely being smashed to bits.
He is rescued by a space-capable civilisation wondering what the heck he is. - Possible, if unlikely. The ending depicts a field of wheat, and since Half-Life and Portal take place in the same universe, this means that the Combine is gone at the very least since the earth clearly isn't After the End, and wheat doesn't grow in fields of nothing but wheat if it is not tended to. Hence it is very likely that civilisation exists, and if it's advanced enough someone would notice the two odd spheres in orbit.
According to the announcer, all turrets have one copy of the Laws of Robotics to share, which is why they still attack Chell. Does this apply only to the turrets built for facility use, or are the turrets that are shipped and sold at retail (which according to supplementary material are available for parents to buy to babysit their children) not given a copy each too?
Cave Johnson's last message comes into play when you think of what he's saying. When he says he wants Caroline to be in charge of the facility, he may have meant that he wanted her to take his place in running the facility after his death. However, due to his "put her into the computer, I don't care", which comes off as being something of a screw-it after thought, the Fridge Horror comes into play when you realize that they heard this message multiple times and believed he wanted her being put into the computer from the get go. Cave inadvertently doomed Caroline to become Gla DOS without even being aware of it.
The 'Hard-Light Bridges' are expressly said to use daylight "piped" from the surface, and yet somehow they still work at night.
Twice as much daylight as is needed gets piped in, with the surplus daylight powering the Bridges at night.
Energy cannot be created or destroyed, yet the Portal gun can give you infinite energy if you place portals above and beneath you, while the Long Fall Boots either destroy as much kinetic energy as necessary or store ridiculous amounts of energy that are never removed. It takes some mental gymnastics to justify.
The scene where you fire a portal at the moon perfectly takes into account the speed of light delay. Except for the fact that the portal gun's "projectile" fires at a speed that is noticeably non-instant to human senses when fired over just the few hundred feet length of a single test chamber. The actual delay before that portal opens should be vastly longer than a speed-of-light delay.