"Woo-oo!": Scrooge's exploit where he exposed the Chupacabra as a shaved bear. This is clearly a reference to the 2010 studies which revealed that the corpses of alleged US Chupacabras are actually of coyotes afflicted with mange.
"The Missing Links of Moorshire!":
Scrooge mentions King James II banning golf in Scotland.
Kelpies are identified by spotting their wet manes (which may also have water weeds stuck in them), which is how Webby exposes Briar and Bramble.
"The Spear of Selene!":
Zeus is most famous for being the king of gods and the god of lightning; but in the myths he's also the god of Sacred Hospitality, something often not mentioned in pop culture. He also had a fragile ego and a vindictive streak, and would be very arbitrary as we see in the episode.
The message outside the Garden of Selene is written in Greek, and does roughly translate to what Webby reads out.
Ligeia and Charybdis are actual names of a siren and a huge-mouthed sea monster, respectively, from Greek mythology.
Storkules's affection for Donald is extremely homoerotic. The mythological Hercules had male as well as female lovers.
"The Other Bin of Scrooge McDuck!": It may seem odd that Scrooge includes a unicorn among the "bad stuff" that has to be locked away, but in mythology, unicorns were indeed often depicted as extremely fierce and dangerous creatures, which Carl Barks accounted for in the original story. Sure enough, this unicorn attacks the girls on sight.
"The Secret(s) of Castle McDuck!": Contrary to what they're most famous for, The Knights Templar mostly acted as the unofficial bank of the church (until they were brutally dissolved and their money confiscated). Scrooge's treasure hunt this episode is about finding the Knights Templar's hidden treasure vault.
"The Depths of Cousin Fethry!":
Hydrothermal vents do in fact release toxic minerals, as Fethry points out.
Huey refers to the mutant sea worm as a polychaete, the annelid class mainly consisting of marine worms. The mutant sea worms also bear resemblance to the deep sea tube worm, a member of the class.
Huey identifies the lab as being in the bathypelagic zone. He and Dewey then encounter a vampire squid, which is found in the bathyal zone.
"The Town Where Everybody was Nice!": Webby identifies the plant as Drosera acidendum. Drosera is a Real Life genus of carnivorous plants (although, obviously, no Drosera species is this big or this intelligent, and there's no species named D. acidendum).
"Last Christmas!": Wendigos are portrayed as lost souls turned by obsession and desperation, which is closer to the original mythology where they are the personification of greed and selfishness, as well as starvation (their infamous Horror Hunger, however, is Adapted Out, for obvious reasons). And sure enough, one of the Ghost of Christmas Past's first steps in becoming a wendigo is to selfishly keep Scrooge in the past for himself.
"Whatever Happened to Della Duck?!":
As if devoted fans didn't already recognize the "Moon Theme" from the NES video game based on the series, the closed-captioning writer even identified it exactly as such.
The crew actually worked with disability experts such as Amputee America to figure out how to make Della's mechanical leg as realistic as possible.
There's also the way the moon's skyline is portrayed during the Time-Passes Montage.
"The Outlaw Scrooge McDuck!" Fenton having a cowboy ancestor, Sheriff Marshall Cabrera. Many historical cowboys were indeed Latino.
"The Duck Knight Returns!": Despite being stereotyped as light and pure good, swans are actually ferocious and dangerous waterfowl. This is reflected by Alistair Boorswan's aim for a Darker and Edgier take on Darkwing Duck.
"Whatever Happened to Donald Duck?!": The scorpion-like moon creature glowing a faint blue in the dark in contrast to its green color under normal lighting. This is a reference to the fact real-life scorpions will glow in the dark under moonlight.
"Nightmare on Killmotor Hill!": Lena turns into a monstrous version of Magica with her arms transforming into membranous wings resembling a mix between bat and pterosaur wings. Occasionally, she would drop down on all fours with her small wing fingers set on the ground, mimicking the quadrupedal gait of bats and pterosaurs.
"Timephoon!": The episode corrects many of the outdated paleontological aspects seen in the original show.
Huey correctly points out that Paleolithic people didn't have wheels or clubs, in contrast to the stereotypical portrayal of cavemen which was present in the original show. (Bubba's capability of using both wheels and clubs showcases how advanced he is.)
Huey is also correct about that non-avian dinosaurs and early humans lived millions of years apart, averting the Hollywood Prehistory trope that was also present in the original show.
Bubba is portrayed as a Genius Bruiser rather than Dumb Muscle like in the original. This is more in line with real-life prehistoric people (including Neanderthals) which were just as intelligent as their modern counterparts, in contrast to the common perception of cavemen as extremely slow-witted.
Instead of a cave, Huey uses an animal skin hut as a reference for his replicated Stone Age shelter for Bubba. In real life, early humans sheltered mostly in huts than caves, as the latter are rare.
Recent genetic studies have shown most non-African modern humans are partially of Neanderthal ancestry, due to interbreeding of Homo sapiens and Neanderthals in the past. The Neanderthal-like Bubba being an ancestor of the McDucks may be a reference to this fact.
Tootsie is correctly depicted with erect hindlimbs and an elevated tail like an actual dinosaur, instead of semi-sprawling legs and a dragging tail like in the original series (although her front limbs would be spread out and her relatively short tail would droop, which may have been the case for Triceratops in real life). Additionally, she is implied to be warm-blooded, as dinosaurs are now believed to be, since she is very active during a storm when there is no sunlight for warming up.
"Moonvasion!": Scrooge paraphrases the Scottish proverb "Twelve Highlanders and a bagpipe make a rebellion."
"Challenge of the Junior Woodchucks!":
Huey identifies the rubber plant by a sign that says its actual scientific name: Ficus elastica.
The Nandi bear is depicted as a Mix-and-Match Critter between bear and hyena, fitting into the cryptid's description.
The woodpecker Violet uses to get off of the tree is properly drawn with two toes in front and two in back.
"Louie's Eleven!": Instead of the upright kangaroo-like stance as in the original series, the Tyrannosaurus skeletons are correctly shown in the horizontal bird-like posture with running legs and a raised tail, which Jurassic Park cemented in the public's mind.
"Astro B.O.Y.D.!":
The episode has great detail in depicting Japan and its culture.
As he and B.O.Y.D. are touring the show's version of the Tokyo Imperial Palace, Huey was about to explain that ninjas were all but extinct. Ninjas mostly disappeared during the unification of Japan in the 17th Century, and the Tokyo Imperial Palace was built in 1888 (on the sites of the Edo Castle which was destroyed by fire in 1873).
Crows are known to be able to hold grudges, and ones living in Japan are more aggressive than their western cousins. Inspector Tezuka fits well in this regard, with her belligerent personality and being unforgiving towards robots ever since Tokyolk got destroyed by one, specifically B.O.Y.D.
"The Rumble For Ragnarok!": The writers had to do a lot of research to make sure everything about wrestling in this episode was accurate.
"The Phantom and the Sorceress!": Rattlesnakes are depicted living in a bog and climbing trees, both of which are known in some species of real-life rattlesnakes.
"They Put a Moonlander on the Earth!": Webby is correct that caterpillars literally melt into butterflies during their pupa stage (they produce enzymes which digest almost their entire bodies, leaving only the stem cells for the wings, antennae, vital organs, and other features).
"The Trickening!":
Webby states that in Celtic Mythology, Halloween was a holiday where Celtics wore monster costumes to scare off demons, and candy was their tribute. It's still different from the real-world history of Samhain, the Celtic festival that served as partial inspiration for modern Halloween, but closer than most American media put it.
Rather than the mindless and lumbering Hollywood version most people are familiar with, the show's version of Frankenstein Monster is a fast-moving Genius Bruiser more in line with the original novel, even if he is a Third-Person Person. He also has the pale skin, misproportioned body, and jaundiced eyes of his book counterpart, and lacks his Universal counterpart's trademark electrodes.
The vampire has both fangs and fang-like incisors like real-life vampire bats, albeit the incisors being exaggerated.
Scrooge refers to "guising" rather than trick-or-treating, which is the Scottish name for it.
"The Forbidden Fountain of the Foreverglades!":
The alligator Webby fights off is depicted with the broad overlapping jaws that differentiate alligators from crocodiles. This is in contrast to most alligators in Disney animated works, which are drawn with more croc-like features like pointed jaws and interlocking teeth.
Webby getting the alligator to back off by hitting it on the snout. Crocodilians have sensitive receptors covering their snouts, hence why it's recommend to attack the snout to survive an attack.
The Noodle Incident that took place on Oak Island in '73. Oak Island is indeed the home of a famous mystery, and possibly treasure...and every attempt to solve/claim it has been a boondoggle, so it's no wonder Scrooge and Goldie don't remember the event fondly.
As with many conquistadors, Ponce de Leon was a ruthless and greedy man due to his various crimes against the Indigenous peoples of America. It doesn't seem unreasonable to portray him as the villain.
"The New Gods on the Block!":
Unlikemost pop-cultural depictions, Hades is portrayed as more true to Greek Mythology, being a fairly benevolent ruler of the Underworld who takes his job seriously.
Like in the original Greek mythology, those who are Swallowed Whole by a titan are imprisoned inside their stomach without being digested. For bonus points, the titan Crownus is named after Kronos, Zeus's titan father who swallowed Zeus's siblings only to be tricked by his son into coughing them back up.
"The Fight For Castle McDuck!":
The McDucks' dinner includes black pudding, a kind of blood sausage made from the leftovers of a slaughtered pig out of Scottish frugality, and they use the Scots term "tatties" to describe potatoes.
Matilda's emu is drawn with visible ear holes.
"How Santa Stole Christmas!":
Reindeer are depicted with long facial hair, which reindeer or caribou develop during the winter for insulation. They also resemble real-life caribou rather than white-tailed deer like in many Christmas specials, although a previous Disney work got this one right.
The episode remembers that female reindeer possess antlers like the males, with Dewey referring to one of Santa's reindeer as a "she".
Reindeer harnesses are drawn with the burden on the animal's shoulders, as opposed to the neck commonly seen in Christmas works (putting the burden on the neck would strangle the animal).
"Beaks in the Shell!": The Noodle Incident where dolphins attacked a party boat as the result of a failed sea projectiles experiment. Bottlenose dolphins have violent tendencies and have been reported to attack humans, contrary to the usualreputation of dolphins.
"The Lost Cargo of Kit Cloudkicker!": When Rhinokey knuckle-walks, his thumbs do not touch the ground like on real gorillas which have thicker hands and wrists to support their weight.
, and possibly treasure...and every attempt to solve/claim it has been a boondoggle, so it's no wonder Scrooge and Goldie don't remember the event fondly.