* Milo tells Mr. Whitmore that he would stake everything he owns that the Shepherd's Journal is the real thing. When you learn Mr. Whitmore had Milo's stuff in storage before he even agreed to find Atlantis, it turns out this is true. If Milo had RefusedTheCall, he would've returned to an empty home where his stuff was packed away.
* Why are the fireflies near the bridge more aggressive than the ones in Atlantis? [[spoiler: Because the fireflies in Atlantis are in closer approximation to the crystal, making them significantly more benign.]]
* Multiple Leviathans are seen flying about in the opening scene, but what in the pre-Bronze Age world would Atlantis need such massive war machines to fight against? How about the Krakken, seen in the sequel? Which would mean that the blast we see was Atlantis's attempt to destroy the thing? Maybe there were more than one. Or if one of the theories on the WMG page is to be believed, they were at war with R'lyeh.
* Kida's full name, Kidagakash, isn't that hard to pronounce. But Milo, an expert linguist who is fluent in Atlantean, gets his tongue tied trying to pronounce it. It's not his fault; he's just DistractedByTheSexy to the point where foreign languages, which normally come naturally to him, start to trip him up.
* The king of Atlantis appears to be blind. When Atlantis was sinking, he told Kida to close her eyes and look away, but kept looking at the crystal as it got brighter. It's likely the flash that it produced making the shield that saved the rest of the city was responsible for taking his sight.
* At first, one wonders [[FridgeLogic how the King of Atlantis knew that Rourke had a weapon on him if he was blind]]. But then later, you learn [[spoiler: the king had long ago tried to harness the crystal as a weapon. He knew Rourke brought weapons because in his position, he would've brought them too. Crosses into FridgeHorror once it dawns on you that Rourke is the king's ShadowArchetype to some extent.]]
* The King's internal injury would probably not have been fatal - except, of course, that the crystal that powers all the smaller stones' healing power has been taken.
** His death is meant to signify what's at stake for the rest of the Atlanteans if the crystal isn't returned.
* Atlantis is in ruins, as Kida often brings up. Just compare the preserved safe area that was protected from the wave in the prologue to the city during the remainder of the story. Atlantis is still so flooded, Milo and Kida have to swim through uninhabitable parts. It begs the question as to why no one tried to repair the buildings. It's not a stretch to think that after the Crystal was sealed in the chamber, the power keeping the city functioning weakened to the point where they could no longer operate the technology to make big repairs and were forced to abandon large parts of the city as they flooded or collapsed over the years.
* When Milo gives his "it's all about money, huh?" chastisement, all of his friends are in the middle of leaving him behind in Atlantis to die with the Atlanteans, and are subsequently convinced to instead do the right thing because of his speech. They're seen actively changing their minds and walking over to stand with Milo. Except for Sweet. As seen, only moments later, Sweet has been inside the palace tending to the dying king, not among the other mercenaries even though he had originally been part of their plan. The crew was clearly only seconds from driving away before being convinced by Milo, so it can be assumed that they fully intended to leave Sweet behind too. Which can only mean that Sweet had a HeelFaceTurn even ''before'' Milo's speech, most likely right when Rourke punched the king and he immediately tried to help him, saying, "This was not part of the plan." All it took was hurting one defenseless old man to make him forget all about the countless riches he could have had, his nature as a doctor prevailing over all. And that's [[CrowningMomentOfAwesome awesome]].
* It seems strange that the Atlanteans can speak just about every language under the sun and then some, but can't read their own. However, when a human learns their primary language, it's spoken first, and reading comes later. The king notes that Atlantis was at war with other countries, implying that other languages had developed even before Atlantis sank. Among the crystals' blessings seems to be a preservation of mind, given that 8000 years would take its toll on a human mind. Taking into account the arguments on reading a couple sections down, it's possible that the crystals have preserved their knowledge of spoken language, but lack of using the written language has caused those skills to atrophy.
* A blink and you'll miss it example. As the sub is filling with water, Audrey slams the door on at least two fellow engineers.
** FridgeBrilliance: The whole sub was filling up, without that engine door closed, more of the sub would be flooded, and [[TheNeedsOfTheMany more lives would be lost.]]
* Or the fact that the Atlantis they found was only a small portion of the whole continent, or even the original capital.
* Most of the Atlanteans are most likely hundreds of years old, and it's heavily implied that this long age is granted to them via the giant crystal under their city. It's certainly proven that the crystal is all that keeps them alive. Now, if Rourke had succeeded in stealing it, what exactly would have happened? Everyone would have aged to dust? Or would everyone have just fallen over dead?
** Maybe they'd just start aging normally from that point? Still FridgeHorror since because they normally life for a very long time, they're not prepared to have children at a population sustaining rate for their new lifespans, including at best a 40 year window for the women.
** It's never stated or implied Atlanteans of non-royal blood have the same aging process as royalty. Children are seen in Atlantis, so they're clearly still having children at a population sustaining rate. It makes sense for only the royalty to age extremely slowly, since the crystal needs them and if the commoners are still having children without eventually passing on, Atlantis would be grossly overpopulated.
* Milo's surface life is effectively ended before he leaves on the mission: his books are in storage, his clothes are packed, and his resignation has been sent. It's implied he has little to no relationships, so that's fine, too. But he never sees his cat again. Either Audrey or Whitmore adopts the cat, since it's sitting on her lap in the last scene in Whitmore's house.
* Before he dies, the King of Atlantis gravely warns Rourke and his crew about taking the (very angry) God crystal. We find out why [[BodyHorror when Rourke gets cut by a crystal shard.]] Had Kida/the Crystal reached the surface, countless others might have suffered this fate.
* The king says that the reason the city sank was because he tried to weaponize the crystal. How it would work is never shown, but whatever it did caused a mushroom cloud and a tsunami. Now consider that this movie takes place in 1914 and the first World War had just begun...
** Helga subtly [[LampshadeHanging Lampshades]] this when talking about the crystal's unequalled power. "I can think of a few countries who'd pay ''anything'' to find out..."
** And on that note, think about how the Crystal reacts when it senses evil or danger, as well as the uncalculated amount of power it possesses. Given the King's warning, and how Crystal/Kida just seems to ''allow'' herself to be captured, what if she was planning to obliterate the crew, along with a good chunk of the western coast, once they reached the surface?
* The Leviathan is still functional somewhere out there deep in the ocean, and it's also implied from the beginning of the film that it might not be the only one out there. If Milo and the Atlanteans can't figure out a way to control it, it would be a nightmare for seafarers or deep sea explorers everywhere, both during the film's time period and in its future.
* When the toddler Kida loses her toy at the beginning of the movie, as they flee the incoming destruction, her mother says not to go back to get it because there's no time. She ''kneels on the ground'', calmly and slowly explains this to her daughter, and takes several more seconds than it would have taken for Kida to actually dash back and grab her toy. She prioritizes reassuring her daughter because she knows this may be goodbye.
* Generally knowledge becomes lost because those who had it die out without passing it on. The Atlanteans are effectively immortal. What, everyone ''forgot how to read''? Why?
** Wrath of the Gods?
** [[HolyIsNotSafe Probably out of fear of the same knowledge and technology that destroyed their civilizations]]. Likely the King suppressed all forms of knowledge for fear that some upstart could discover the secret of the Heart of Atlantis and cause yet ''another'' disaster. Therefore, the Atlantis that we see is losing all knowledge of its own cultural identity, its people are kept blissfully ignorant of their own cultural identity, and very likely have forgotten, or never even learnt, how to read in the nearly 9000 years since the flood.
*** The [[AllThereInTheManual Summer 2001 issue of Disney Adventures]] mentioned that he had the library closed off.
** The ''royal'' Atlanteans are effectively immortal, aging extremely slowly and having extremely long lifespans, presumably because the crystal needs them, but the commoners are never stated or implied to be the same. Besides, Atlantis would be grossly overpopulated if that were the case, since Atlantean children are shown. Also, Kida was very young when Atlantis sank, so it's possible she never learned to read while the rest of Atlantis forgot over generations, and it's no stretch the king made decrees which Kida was too young to remember.
* How could Rourke have known which page of the Shepard's Journal, that contains the exact details of the "Heart of Atlantis", to tear out if Milo's the one that can read Atlantean?
** Illustrations on the page?
*** Agreed. That page had a great big shiny star-diamond thing on it that took up almost half the illustration. It's not hard to figure that's the most important moneymaker in the quest.
** Milo didn't learn Atlantean in a vacuum -- his grandfather, Rourke's old companion from the Iceland expedition, taught it to him. There's every possibility the elder Thatcher inadvertently told Rourke of the importance of that section of the journal.
* When Milo slides off the blackboard at the beginning to take care of the boiler, the chalk stays on. But when he slides off the second time, he indeed does clean it off.
* So the movie needs a group of heroes for the finale, but is it not out of character that the mercenaries are suddenly squeamish about making the biggest payday of their lives? How is killing people not part and parcel of a mercenary expedition like this? Did they not ever expect to kill anyone as mercenaries?
** Probably because it involves mass genocide instead of open combat or grave robbery of a long dead civilization.
** Even most mercenary companies, who accept that they will be killing enemy soldiers just to get rich, generally recognize that it's not ''right'' to strand non-combatants in a situation that will inevitably kill them. EvenEvilHasStandards / EveryoneHasStandards is pretty common for a reason.
** Not to mention that when they are received by the Atlanteans, Helga says that there wasn't supposed to be people in Atlantis and that that changes everything for the operation. She even looks a bit unpleased when Rourke just says it will all remain the same.
** Given Vinny's KirkSummation to Rourke, and Milo's attitude when he calls Rourke a mercenary, it's entirely possible that's just an insult. The majority of the group seems to be glorified thieves rather than actual guns for hire.
* Kida mentions to her father that the previous kings would weep if they could see how Atlantis has fallen, and later she falls to her knees to pray to their stones around the Crystal. But, Kida's 8500 - 8800 years old and she looks like she's in her late teens - early twenties - how old is her dad? And how old were "the kings of our past" - how long has Atlantis been around?!?!
** King Kashekim is apparently about 27,000 years old, according to official material, and there's eight or so carved faces around the crystal. Assuming they're all previous kings, and lived as long as Kashekim... Something tells me that after Atlantis surfaces in the sequel, the history of the evolution of man is going to need a little reworking...
* Why did the Crystal even need a person to fuse with? Especially the second time, when fusing with Kida only made the situation worse by making the Crystal able to be captured (it didn't even fight back or anything). And why did the Crystal give back Kida at the end, when it didn't give back her mother? Why ''didn't'' it give back her mother?
** Her mother was connected to it for too long. The king said that if "Kida remains bonded to the crystal for too long, she will be lost to it... Forever." So presumably her mom was just bonded to it for a bit to long when it sank the city and the crystal just absorbed her.
** That, and with Kida, all it needed to do was turn on the shield. With her mother, it had to turn on the shield, sink the city, create an air bubble in the upper mantle, AND generate an endless suply of fresh drinkable water. Logically, the latter would require a lot more power than just activating the guardians for the shield.