Any stock horror scene where all the animals in the forest are apparently ganging up to scare the protagonist by making startling cries for no reason, often at night. While forest ambience does include many animal sounds, the presence of a person in the woods would usually lead to the animals falling silent, since they don't know what that weird two-legged ape is doing there and may take it as a threat.
Predators roaring as they attack their prey. Roaring is usually a territorial behavior meant to scare off rivals, but predators tend to shut up when they're hunting. After all, what sense is there in scaring off your prey and defeating the whole point of sneaking up close enough to catch it?
Mammals
Though the idea that giraffes cannot make any sound at all seems to have been discredited, they are still very silent creatures. This is apparently disliked by filmmakers, who makes them sound like... rhinos (one example: Gladiator - the giraffes make the same sound as the baby Stegosaurus in The Lost World: Jurassic Park, which in turn sounds just like the audio sample in Encarta's entry on the Black Rhinoceros). In reality, giraffes make sounds such as snorts, hums, and bleats, which do not sound anything like a rhinoceros.
African elephants frequently use recordings of their Asian counterparts in film. This is likely due to the fact that fewer African elephant recordings exist in public domain sound effects libraries.
When a rat appears on screen, it will squeak. Real rats squeak very rarely, usually when fighting. They are very vocal, making lots of clicks and chittering noises... most of which are too high-pitched for humans to hear.
Also, ANY rodent will squeak, even if it's a rodent that makes another noise, like guinea pigs. Guinea pigs have a rather wide range of sounds, but the closest thing to squeaking is when they wheek. And whereas a squeak is usually a small sound, a guinea pig's wheek is more like a loud yelling when they want attention. Here are some of the sounds guinea pigs make, and you can almost guarantee you will never hear them when a guinea pig is on-screen.
The sounds of any ape, and most monkeys, are commonly represented by the hoots, grunts or screeches of chimpanzees. This is particularly noticeable when it's used with gorillas, as even if you've never heard their real voices (deep rumbles, pant-hoots, and yawn-like grunts - plus the roar of a silverback), sheer bulk makes a chimp's cries seem incongruously high-pitched. The Disney adaptation of Tarzan is particularly guilty of this.
In Fictionland, all big cats smaller than a tiger and lion almost always utilize the iconic caterwaul of the cougar. Even species that are just as capable of roaring as lions and tigers, specifically the leopard and the jaguar, get this treatment, even though they make no high-pitched screams akin to the cougar's iconic scream, as seen here. Like with the frog example, the fact that the cougar is the only big cat, and the only other wild feline besides the bobcat, found in California likely contributed to the prevalence of this trope. Smaller cats like ocelots and lynx have their own unique vocalization, which can sound rather scary on their own terms.
Conversely, in some works, cougars themselves may emit roars like pantherine cats. Cougars (or mountain lions, or pumas, or whatever else you call them) are among the largest of the Felinae or small cats, and lack the physiology required to roar like a big cat does (the hyoid bone in the throat is not properly shaped for that, for instance).
Lions themselves are often portrayed emitting louder, more explosive snarls like tigers. Actual lion roaring usually sounds like this. A lion's snarl sounds like this.
In addition, lions are even more frequently portrayed emitting a peculiar kind of snarl that actually comes from an African leopard.
On that note, having a cheetah make standard feline vocalization, whether it be big cat roars or cougar screams, cheetahs are well known for having very.......unconventional vocalizations for a feline ; they chirp like birds, bark/yap like foxes, make high pitched calls and "churrm".
Hyenas barking, howling, yelping, growling or whimpering in a canine manner, as heard in The Lion King. Despite appearances, hyenas aren't dogs (they`re closer to mongooses and even cats) and they don't make any canine sounds. They have a unique plethora of vocalizations that depends on the species. Spotted hyenas make grunts, whoops, groans, a very rattling snarl, and of course their iconic laughing cry; striped hyenas, on the other hand, sound like this.
Large cetaceans are often associated with the vocalizations of humpback whales. This is especially jarring when it's used with orcas, which are dolphins and thus make squeaking, whistling, or clicking noises.
Seals and walruses are depicted making barking sounds like California sea lions; in truth, other seals make very bizarre groans, while walruses emit deep bellows and grunts. Oddly enough, walruses can also whistle.
Because rhino vocalizations are rare in sound libraries, whenever a rhino shows up in fiction, they’ll use the vocalizations of other animals, most often the grunts, bellows, and growls of cattle and buffalo. Granted, this isn’t too far off the mark, as rhinos can make similar vocalizations (despite being more closely related to horses), mainly during shows of aggression, but they are also known for making high-pitched wails, whoops, and squeals, despite their sheer bulk.
Birds
The default noise made by any bird of prey, especially the Bald Eagle, is in actuality the cry of a Red-tailed Hawk, a long, drawn out, and majestic-sounding call. This is so damn pervasive that it shows up in places where the producers really ought to know better. The station IDs for Animal Planet, for example. For the record, a Bald Eagle actually sounds like this. Just to bring things full circle, there have been a few instances where this is used for the cry of a Red-Tailed Hawk.
It's really easier to list the aversions and weirdest examples:
Mostly averted in Disney's Brother Bear, where Sitka sounds like an actual eagle - except for the grand crescendo at the end, where he once again became a hawk in disguise.
One of the most confusing instances of this was an episode of Alvin and the Chipmunks where the baby Bald Eagles made genuine eagle calls but their parents sounded like hawks.
In the Haruhi Suzumiya episode "Remote Island Syndrome Part 1", there was a gull with the call of a red-tailed hawk. While gulls can indeed scream, they obviously don't sound like that.
And in Binchou-tan this cry is uttered by a duck. It is also delivering mail at the time, so its cry is perhaps the least odd thing about it.
Justified in The Rescuers Down Under: Marahute is a fictional species (who seems to have been born fully fledged out of the Rule of Cool) and is voiced by a human (the extremely versatile Frank Welker).
And in K-On! the cry is yet again used for a seagull during the obligatory Beach Episode, maybe as a Shout-Out the aforementioned Haruhi Suzumiya episode, which is produced by the same studio.
Actively averted in anime with the black kite, which is a mid-sized bird of prey found throughout Japan, and whose distinctive call can often be heard during scenic moments.
Common Loons are very large, somewhat rare aquatic birds who are also known as The Great Northern Diver. In reality, they tend to be heard almost exclusively around their natural habitat: large bodies of open water in cold parts of the Northern Hemisphere. According to movie logic, they are everywhere. Even shallow swamplands, the middle of a forest, the middle of a mountain range (!?!), Craphole Island, and Thra, the world where The Dark Crystal (in which a modified loon call was used for an alien bird) takes place. Their cry is evocative, so Rule of Cool can make some instances work - as long as they're believable.
Crows and Ravens in horror movies tend call out in the dark of night to offer a scarier atmosphere. It seems these birds suffer mean cases of insomnia and have nothing better to do, because corvids are mostly diurnal — like humans, they can't see well in the dark, and a lot of the animals that prey on them are active at night.
Every owl in the world goes "hoot". Every single one. Except for the Screech Owl. They must certainly make a blood-curdling scream as advertised (see My Cousin Vinny). Not, you know, a distinctive trilling or whinnying. In reality, the owls that make bloodcurdling screams are Barn Owls.
All seabirds in fiction sound like herring gulls regardless of species. And every seashore in fiction has them calling in the background, regardless of location or season.
Regardless of gender, all ducks in fiction quack, especially making the sound of a mallard. In reality however, only the female can quack properly, whereas males tend to make a raspier "squack" sounding noise.
The trope of the Silly Animal Sound often leads to all sorts of birds making clucking and squawking noises like a chicken (or the crowing of a rooster whenever the sun rises), particularly in more comedic moments or works, regardless of if the bird in question does or doesn't have the right vocal organ structure to make such sounds. Those are about the only chicken noises you'll get in fiction, too — never mind that chicken vocalizations are much more diverse in reality.
Reptiles and Amphibians
Not-rattle snakes somehow doing the rattlesnake sound. Gophersnakes, although they don’t have rattles, may mimic the sound of a rattlesnake’s rattle, along with having colors similar to rattlesnakes, in order to mimic a rattlesnake. Makes less sense for other non-rattle snakes though.
The Pacific tree frog is the only kind of frog that produces the "ribbit" sound. It's native to California, which is why Hollywood believes frogs everywhere in the world go "ribbit". There are, technically, a few other amphibians in America whose song sounds like ribbiting - but they're toads. Other species of frogs tend to make chirping, burping, beeping, or trilling calls.
There's a species on the east coast around the Carolinas that very clearly says "HNAAAAGH!" with a volume out of all proportion to its size.
In Japan, frogs go "kero kero".
Bullfrogs call for "Rrrrrum" and Green Frogs call for "Doug"!
It's surprisingly common for fictional sharks to let out a growl as they open their mouth for a bite. Granted, the Draughtsboard shark does produce a "barking" noise when caught (hence its nickname of "barking shark"), but this is due to inflating its stomach with air first to try and make itself look bigger because, ironically, the shark itself is under threat. Sharks otherwise lack any kind of organs to produce sounds at all, being specialized for sneaking up on their prey in complete silence.
Insects and spiders, especially Big Creepy-Crawlies, are often shown hissing, shrieking, or even roaring through their mouthparts. Arthropods breathe through spiracles on the sides of their abdomens and do not vocalize like vertebrates do. Any noises they do make are usually done by stridulation, i.e. rubbing certain body parts together. This is most famously done by crickets, but unlike what some believe, only the males do so.
In the same manner as fish, fictional cephalopods tend to gurgle or "bloop", and Giant Squid may even utter a Mighty Roar. Not only do cephalopods lack any vocal organs at all (nor can they even hear in the conventional sense), but octopuses especially are adapted for concealment, so any means of making sounds would be worse than useless for them.
frequently use recordings of their Asian counterparts