Dodos never went extinct. They're actually magical birds called diricawls and are capable of teleportation.
The Loch Ness Monster is actually a shapeshifter, and hides whenever Muggles try to look for it.
Some rhinos are actually erumpents, whose horns explode upon touch.
Some Jack Russel Terriers are actually Crups, which usually have two tails but often have the second tail clipped so they can blend in.
Muggle children have often been accused of vandalising or destroying a back garden - when an offended Knarl is the culprit.
Crop circles are caused by Mooncalfs doing their mating dance in fields of wheat.
Breath Weapon: The Nundu's breath - which causes disease strong enough to depopulate entire villages.
Brown Note: Fwooper song, if listened to too much; eyes of a Basilisk. The cry of the Augurey was thought to be this but that's just superstition. The cry of the rooster is this for the Basilisk.
Call Forward: Rita Skeeter claims that Hagrid's Blast-Ended Skrewts are illegal crossbred creatures in the fourth book. Their lack of an entry in this one confirms that.
Cassandra Did It: Augureys are feared because their cries are said to cause death. In reality, they're just predicting rain.
Character Filibuster: Ron and Hermoine get into a large argument... via notes... on one of the first pages of Harry's books. Harry tells them both to shut up.
An entry right next to trolls has a drawing of one of Malfoy's goons, courtesy of Ron.
My name is Gregory Goyle and I smell
Comically Missing the Point: Hermione points out that Ron could have used the money he wasted on Dungbombs to buy a new book for himself. He replies with "Dungbombs rule."
The Complainer Is Always Wrong: It's common to find a Runespoor (three headed serpent) with the right head bitten off - as this head is 'the critic' and criticises the other two's actions.
Continuity Nod: In the entry for the hippogriff, there's a brief line stating that they can be tamed, though this should only be attempted by experts. Harry's remark? "Has Hagrid read this?"
The entry for the Kappa, a Japanese creature that Snape claimed was more commonly found in Mongolia during Prisoner of Azkaban. "Snape hasn't read this either."
The entry of the Hungarian Horntail describes it as the most dangerous dragon breed of all: Harry noted "You're not kidding".
In the entry on Acromantulas, there's a note about rumours of a large colony established somewhere in Scotland. It's crossed out with "confirmed by Harry Potter and Ron Weasley" written over it. This also confirmed to many fans that Hogwarts was located in Scotland.
Hagrid at one point tells Umbridge he has a friend that breeds Abraxan Horses. This book gives the name and information of them - enormously powerful and palomino bodied - which confirms that Hagrid is talking about Madam Maxime. And that they are the horses that carried the Beauxbatons carriage.
Dark Is Evil: Any beast or being classified as a "Dark Creature" falls under this. Dark Creatures (or "Demons" as they are classified) consists of anything that is capable of magic and uses said magic for the sake of malicious intent rather than survival. Dementors, werewolves, and boggarts are all considered Dark Creatures whereas chimeras, manticores, and dragons are not. This is because a dragon will only attack a wizard (or Muggle) to defend itself or for food while a werewolf will attack to turn another human into a werewolf or out of murderous intent.
Dark Is Not Evil: The Thestral has a black coat, has a very reptilian appearance, is attracted by raw meat and is considered a bad omen - because it can only be seen by those who have witnessed someone die. However that is just superstition and the horses in the series are perfectly friendly to Harry when he meets them. Likewise the Augurey was thought to be an omen of death, when it really just predicts rain on the way.
Darkest Africa: Africa does sure have a lot of dangerous dark creatures such as the Nundu, Tebo and Streeler.
Deadpan Snarker: Have you read Harry and Ron's commentary? There's also the arguments Ron and Hermione get into.
Early-Bird Cameo: Many creatures first appeared here before being mentioned in the books. Even Thestrals are included, albeit as a minor reference under "Winged Horse". Likewise some creatures that appeared but weren't named, were given official names in this - such as the Acromantula and the subspecies of Merpeople and Winged Horses.
Then there's the erumpent, a rhinoceros-like creature that has an exploding horn. In Deathly Hallows Xenophilius Lovegood has one's horn on his wall (thinking it belongs to a Crumple-Horned Snorkack) and his accidentally blowing it up helps the trio escape.
Emotion Eater: The Pogrebin, which tails humans for hours and causes them to feel despair. Luckily just kicking them is pretty effective in getting rid of them.
Exact Words: Early definitions of "Beings" were done with human centrism in mind, leading to definitions like "creatures who walk on two legs" or "who speak the human language." This would leave out obvious beings like centaurs and merfolk, but accidentally include a lot of creatures, such as trolls, augureys, fwoopers, or vampires. Havoc ensues. The definition that stuck was "Any creature that can understand the laws of the Wizarding World", which helped tighten the list to just sentients.
The Fair Folk: The pixies definitely. The doxy is also quite the little pest.
Foreshadowing: The Demiguise is mentioned as a huge, gorilla-like creature whose silky hair is used to create invisibility cloaks. These cloaks are said to wear out over time. Harry's cloak has been around for years and is still fully functional, becoming an important plot point in Harry Potter and the Deathly Hallows.
Footnote Fever: Not just from the author, but from Hermione, Ron, Harry, and various others. If it's from the gang, expect it to be arguing, nitpicking, or Harry telling Hermione and Ron to stop arguing.
Gentle Giant: The Sea Serpent, which is surprisingly benevolent.
Giant Spider: The Acromantula. It's theorised to have originated from experimental breeding - as it is capable of human speech.
Not the Nessie: There is one, but it's part of a larger species, and is a shapeshifter - it turns into something else whenever muggles look around for it.
Our Dragons Are Different: The book obviously depicts every single species of dragons in the Potterverse. Most seem for some reason to be European (even the South American and Australasian species), with only one species based on Chinese dragons, and even so being more akin to European forms as it breathes fire and is malevolent (although all of them are more animalistic than anything, harkening back to the pre-Tolkien versions of the myths).
Our Fairies Are Different: Five particular creatures. All of them also lay eggs like insects rather than giving birth to live offspring.
Fairies - the traditional tiny cute Winged Humanoid. Has very little intelligence and very basic magic. Usually just used for decoration. The author expresses surprise at the good Muggle press the Fairy has.
Pixie - tiny shrill flyers. They love making mischief and are strong enough to lift a human's weight.
Imp - close cousin to the pixie, but much duller in appearance and cannot fly. Also considerably less of a nuisance.
Doxy - covered in black hair, with two sets of very sharp teeth and extra arms and legs. Considered pests, they're also very hostile to humans.
Bowtruckle - a tree-dwelling creature that appears to be made of wood. Is normally benevolent but will get violent if it is threatened.
Our Griffins Are Different: Classical griffins and hippogriffs (note that hippogriffs were a part of mythology, but mostly as a figuratively unlikely creature, since horses and griffins were enemies).
Our Mermaids Are Different: And there are three species of them - Sirens, Selkies and Merrows. Selkies are the only ones that actually appear in the series though. The Mermish language sounds like a lot of shrieking and screaming above the surface. But underwater it sounds like normal talking. All merpeople are said to share a great love of music. They presumably can't transform into humans at all.
Another creature - the Hippocampus - has the head and forequarters of a horse but also has a fish's tail. It's not classified as a merpeople species despite the similarities.
Pegasus: Winged Horses are given an entry. Pegasus is even given a nod as helping the only wizard to ever successfully slay a Chimaera. There are four species.
Abraxan - the biggest and strongest, with palomino bodies. These horses appear in the series, transporting the Beauxbatons carriage from France to Britain.
Aethonan - chestnut in appearance and native to Britain and Ireland.
Granian - a greynote Meaning actually with a white coat, confusingly enough and incredibly fast. This would be what species Pegasus was.
Thestral - black and more reptilian in appearance. Is invisible to everyone except those who have 'seen death'. Also very good at finding locations.
The Phoenix: Of course. The Augurey is also known as "The Irish Phoenix".
Playing with Fire: The Fire Crab naturally. It shoots fire out of its ass as a defence mechanism.
Power Trio: The Runespoor is a three-headed snake and the heads form one of these. The middle head is the dreamer (The Id), the left head is the planner (The Superego) and the right head is the critic (The Ego).
The Nundu is described as the most dangerous beast in the world. You would guess that Harry has to fight one later in the series. He doesn't. Then again, it lives in Africa, where Harry really didn't have any reason to go...
Ditto with the Lethifold, which requires a Patronus Charm to repel. Around the time this book came out, we'd only seen Patronuses used on Dementors. Yet no one encounters a Lethifold in-series.
All of these are probably due specifically to the remote location of the beast, Nundus being East African and Lethifolds being tropical, though.
Riddling Sphinx: Despite its humanoid appearance, it gets classed as a beast because of this. It speaks only in riddles and puzzles - and gets violent if given the wrong answer.
Sea Monster: The Sea Serpent counts as a subversion as - despite reaching up to a hundred feet in length - it's a fairly docile creature.
Selkies and Wereseals: In this universe, 'Selkie' is a subspecies of merpeople. It's implied that they are the merpeople encountered in the Second Tasknote They are said to come from Scotland and this same book implies that is where Hogwarts is located - possibly referencing selkie mythology, they have a more aquatic appearance that traditional beautiful mermaids.
Sirens Are Mermaids: 'Siren' is a species of mermaid found in the Mediterranean. They are the beautiful mermaids commonly depicted in art and literature, contrasting with the Selkies and the Merrows - which have more alien appearances. All merpeople are also said to share a love of music - which comes from the Siren myth.
Stuff Blowing Up: Erumpent horns contain explosive fluid. Their numbers aren't very large because of this, as they still have the rhino instinct to charge at poor bastards.
Take That, Scrappy!: In-universe example. The Flobberworm - most despised creature Hagrid ever brought to class - is officially classified as 'Boring' in the book's entry.
Unicorn: Much of the same information we were given in Hagrid's lesson in the fourth book. Foals are born pure gold, then they turn silver, then they grow horns and then they turn white. The tail hair is incredibly strong.
Visual Pun: Fairies are conjured up to serve as decorative lights - fairy lights.