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The Marvel Universe has the mutant Wolfsbane from New Mutants, who had to be reassured she was not a werewolf, as they were considered to be demons where she was from and her wolf like appearance caused her much self loathing.
J. Jonah Jameson's son, the astronaut John, is not a werewolf either but has an alien weapon that makes him look like a wolfman. He is considered a godly savior by said aliens.
There are also books at least three books where they go to other parts of the world (the Amazon, Inuit territory and the Australian desert) and get mistaken for the local legendary spirits.
In The Twilight Saga, Sam Uley and his pack are not werewolves; they are shape shifters who can only turn into wolves. A clue to this is that they shift voluntarily, while werewolves in the Twilight universe can only change on a full moon.
Mercy Thompson is a walker, not a werewolf. Even if she does hang around with them a lot.
The Dresden Files has at least five completely different magical creatures that could be classified as "werewolves," not one of which works in horror movie fashion. Getting them mixed up can potentially be fatal. The trope is averted because they're all referred to as werewolves and there is no Insistent Terminology.
The unstoppably destructive loup-garou, a person cursed to turn into a wolflike demon. If you don't have its one, specific weakness handy, run.
Berserkers, people who can channel animal spirits but don't actually transform. Badass Normal and crazy, but basically human.
Actual werewolves, magic-users who know only one single Voluntary Shapeshifting spell. More dangerous than a real wolf because they have a human's mind, but they don't have the self-control issues of the previous types.
At least one wolf who can turn into a human at will.
Wolf from the Wolf & RavenShadowrun short stories was originally intended to be a werewolf, until the author was told that Weres in that Verse are animals who assume human form, not vice versa. The character was therefore re-written as a human physical adept with an intense — sometimes too intense — spiritual bond to the Wolf totem.
As one of the ridiculous questions she has to discuss with her opponent, Eija Semezou is asked whether she prefers vampires or werewolves. She protests that the layman's terms are too vague for a response.
Some of the local goths mistake Eija and Hel for various supernatural creatures. They're actually underestimating.
In Wolf in Shadow Rhian can transform into a wolf and people assume that she is a werewolf. Actually, her ability comes from an ancient Celtic brooch which is infused with the power of the sorceress/goddess Morgan le Fay who was the queen of shapeshifters. A character more familiar with supernatural matters concludes that this more closely resembles demonic possession and derives from ancient elf/fae magic. Werewolves are said to exist in that universe but their characteristics are not discussed. Ironically, a Totally Not a Vampire character assumes that she is a powerful witch who found a way to use wiccan magic to shapeshift.
Totally Not Vampires are referred to as "suckers". While they feed on life energy contained in human blood and are damaged by sunlight, they are quite different from stereotypical fictional vampires. The people who have to fight them use inisist on the name "sucker" to remind everyone of the differences.
Oddly inverted in A Wolf In The Soul. Greg fits the standard werewolf tropes a lot more than do the species of werewolves described in the mythology, of which he is not a member.
Live Action TV
Happens all the time on Doctor Who, although it is possibly a subversion. The Doctor has admitted he makes up some of the technobabble because he doesn't want to say "It's magic" so a "Lupine Wavelength Hamaevoform" fits the Not Using the Z Word aspect of this trope. Also, the various Vampires from Curse of Fenric, Smith and Jones, Vampires of Venice, State of Decay, etc.
Supernatural introduced "skinwalkers", who can transform into wolves (or dogs, at least) and are distinct from the actual werewolves who do transform with the lunar cycle, but into humans with evil eyes and bad teeth. However, they do share a number of characteristics, including the ability to infect people by biting them, and an allergy to silver. Not very surprising, then, that the brothers thought they were hunting a werewolf when they started looking into the skinwalker.
Grimm has "Blutbaden" which are wolf-like Wesen; the term used to refer to creatures on the show.
In The Vampire Diaries, Tyler notices Caroline's abnormal strength and speed and accuses her of being a werewolf like him. She laughs and reveals that she's a vampire instead.
Old World of Darkness: Vampires, werewolves, Pooka changlings, and mages all had powers which could let them turn into wolves. So what happened if you put one of each on a stage to perform this trick in front of mortal witnesses? The vampire gets the expected mundane reaction, the werewolf drives witnesses into hallucinations and denial, the changeling leaves all but the least banal of viewers remembering it as a vague dream, and the mage explodes because the universe doesn't like people turning into wolves.
New World of Darkness too. Changelings, Vampires, Prometheans, Sin-Eaters, and Mages can all access powers that allow them to turn into a wolf or other animal, in addition to the actual Werewolves.
When the 2005 trailer for The Legend of Zelda: Twilight Princess was released, fans and reviewers quickly attached a 'werewolf' label to the depiction of Link being transformed into a wolf. Nintendo did respond saying that only the 'wolf' part was accurate; Link's transformation was revealed to be a Fisher Kingdom effect caused when Link is exposed to the Twilight Realm.
Quest for Glory IV has the gypsies, whom the superstitious townsfolk think are werewolves. Their leader laughs at the idea, saying "Cross my palm with silver; you'll not see me flinch!" The hero has some experience with this, having befriended a tribe of Leopardmen in the previous game.
Inverted in World of Warcraft with Worgen druids, who are actual Worgen, but can shapeshift into other animal forms through druidic spells unrelated to their natural lycanthropic abilities.
Played straight by the fanbase. If you ever ask why Worgen don't have tails like werewolves usually do, this trope name will be the response shouted at you.
Unless you're a Gangrel, instead your character fanboys over his power and asks if he can teach you that discipline.
Sorcery 101 distinguishes werewolves from wolf-demons, which are sort of the opposite: supernatural wolves that can assume a mostly-human form.
Spinnerette has a rather long arc starting out with both the heroes and the villains chasing something that appears to be a werewolf. The heroes end up catching a three headed guardian of the underworld. The villains run into an Eldritch Abomination the former was trying to hunt down. There wasn't a single werewolf involved in the story, unless we count one of the heroes.
Techwolf of the Whateley Universe looks like a seven foot tall werewolf all the time. He's not. He's just under a curse. And Bloodwolf can transform into a werewolf shape because he's a mutant: he's an Avatar who has captured the spirit of the werewolf. However there are real werewolves out there. And Paige has been turned into a werecat. (Werecougar, specifically...)
In fact, the werewolves are the local Native American tribe.
Timberwolf from the Legion of Super Heroes cartoon is one of these, especially when first captured. Lampshaded by Bouncing Boy:
-looks at some scratches on Lightning Lad from Timberwolf-
Bouncing Boy: Hope you don't turn into one of those things.
One Halloween episode of Gargoyles had a mysterious wolf-like animal roaming through the city every night, and Goliath is seen researching werewolves as a possible cause. It turns out it's actually Fox, whose engagement present is an Artifact of Doom. Her fiance Xanatos has no fewer than four plans to get it off of her.
Ben 10 had an episode where Ben was attacked by an alien matching the description of a local werewolf myth, and the previously unknown "collect DNA" function of his Omnitrix activated, slowly transforming him into a duplicate of it. The cast drew the obvious false conclusion.
Examples of being mistaken for other monsters:
Anime and Manga
Shaman King has Boris Tepes Dracula, a descendant of the original Dracula whose family use shaman powers to mimic vampires. Specifically he uses blood as a medium to channel bat spirits, forming a cloak which can split into bats. When he bites someone he absorbs more blood into the cloak while injecting some back in - since this blood is still under his control he can then use the victims as People Puppets.
Arystar Krory from D.Gray-Man is an Exorcist who unknowingly gained an Innocence that takes the form of fangs and compels him to drain the blood of Akuma. Since most of the Akuma he attacked were in human form, he thought he had become a vampire who was killing helpless humans.
In the Marvel Universe anyone with super powers is mistaken for a mutant until their origin is known to the public. (Mind you, people prone to fearing mutants for their powers aren't likely to be comforted by the fact that for you it was mongoose blood instead of inborn.)
In one arc in Fables, the characters' Masquerade is threatened by a journalist who, being Wrong Genre Savvy, assumes that their near-immortality means that they must be vampires.
In Threads of Fate, when Rue transforms himself into a harmless Pollywog to sneak up on some bandits, the girl he rescues assumes that the Pollywog is his true form, and it takes a while for Rue to correct this mistaken first impression.
A frequent point of comedy (and irritation) for Lady Zozo in Code of Princess, who gets called a "zombie" by just about every bad guy she meets. She constantly has to remind them that she's not a zombie, but a necromancer.
Susan: "It used to be human. Some people use magic to try and achieve immortality by turning themselves into parasites. The immortals call them aberrations, and... [beat] You know what? Screw it, it was a vampire."
Sarah: "A vampire?!"
Susan: "No, not really, but it was a monster that used to be human, hypnotized young women and sucked blood out of their necks. It doesn't matter what I say, you two are going to hear 'vampire'."