1. Everyone Loves Anime
While Japan is the home of anime not everyone in the country watches it, or even likes it. In fact, outside the anime capital of Akihabara you'll have a hard time finding people who are into anime. Many Japanese people eventually grow out of watching anime in their teen years and go on to reading manga instead.
The reason for this is because anime is targeted to young teens. There is a lot of anime that is comparable to children's cartoons in the U.S. and it's seen as something childish to watch. While there are a lot of anime sub-genres that contain adult content and themes it still isn't that popular with the majority of the adult population. Of course, there are plenty of Japanese people of all ages that enjoy Studio Ghibli and other animated films just like there are plenty adults in the U.S. that enjoy watching Disney films.
Anime is also heavily geared towards nerds and otaku's. An otaku is someone is obsessed with anime, it's comparable to the western term "super nerd" which is defined as someone who is obsessed with comic books and graphic novels. In the west, being obsessed with video games and comic books has gradually switched from being taboo to trendy, but Japan has yet to make that switch.
I've met many people in the U.S. who proudly claim the title of otaku and brag about how they stay up all night watching anime series. They believe that when they go to Japan they'll be able to talk about anime to everyone around them, but this is sadly not true. Contrary to popular belief, being an otaku isn't cool in Japan, but is in fact frowned upon. Otaku's are stereotyped as lonely men in their 30's who are so obsessed with anime/manga and don't leave their house. Being an otaku in Japan implies that instead of working on finding a job, or focusing on your education, you're wasting your time watching cartoons...not cool.
2. Japan is Like You're Favorite Anime
Many anime fans in the west believe that everything that they see in anime is what people do in Japan, this is obviously not true. Rich students aren't driven to school and no, Japanese uniforms aren't short and skimpy like they are in anime.
Often, you'll see anime characters hanging out on the roof of their school, this is prohibited in Japan and doors to roof are often locked and secured. Students are also not allowed to dye their hair or even wear nail polish to school.
3. Whale and Dolphin is a Popular Meal in Japan
I feel like this myth has been exaggerated by the TV show Whale Wars. While Japanese people do it whale and dolphin meat it isn't as common as you think. Eating whale and dolphin in Japan is as uncommon as Americans eating crocodile and bunny meat.
This myth was also probably exaggerated by the fact that during WWII and a little bit after Japanese people would eat a lot whale meat because it was easy to find and a good source of protein. You can probably find packaged meat in supermarkets around Japan, but it's still not a common meal that Japanese people eat.
With that said, don't go into a restaurant and ask "wheres the whale/dolphin meat? I thought you guys ate that all of the time!"
4. The Age of Consent is 13
This myth really disturbs me because it gives people the idea that Japan is a weird perverted country, but this simply isn't true.
Yes, Japan's official age of consent is 13, but there are a variety of laws that raise it to around 18. The Child Welfare Act in Japan states that any act of "fornication" (sex outside of marriage) with children (defined as being under 18) is forbidden.
The Child Welfare Act also allows individual prefectures to apply there own laws through obscenity statues. This allows, for example, two people under 18 to consent in a sexual relationship if they are in a "sincere romantic relationship", this is approved by the individuals parents.
This may seem a bit complicated, but in short, while the official Japanese age of consent is 13, the Child Welfare Act raises that age to 18 like the majority of the world.
5. Japanese People Aren't Emotional
Japanese people cry, laugh, get angry and smile just like everybody else, the difference is that the Japanese culture puts a large emphases on controlling one's emotions. Japanese society is focused on the group and not on the individual, so expressing negative emotions like anger and sadness in public can be seen as selfish and can make others uncomfortable.
You'll often hear Japanese people say "shouganai" when something negative happens. This phrase is translated as "it can't be helped" and perfectly describes the Japanese attitude towards negative events. Japanese people often brush off bad things like someone cutting them off in traffic, or someone cutting them in line by saying this phrase. While they may not like the situation they choose not to dwell on it because it's outside their control and move on.
While the Japanese don't wear their heart on their sleeve in public they do use body language, tone of voice, word choice and other subtle cues to communicate their emotions. Reading these cues can be very difficult to foreigners because they're used to people freely expressing their emotions, so it's understandable where this myth comes from.
Just like everyone else, however, the Japanese are very open about their emotions to their close friend and family. Of course everyone is different so this can vary from person to person.
6. Slurping Noodles is a Compliment to the Chef
This is a very common myth in the west that slurping your udon or ramen noodles really loudly is a compliment to the chef in Japan, but in fact it isn't. While slurping your noodles isn't really big deal in Japan it's by no means a compliment to the person who prepared your meal.
The reason Japanese people slurp their noodles is because dishes like ramen are served hot and you're supposed to eat it as soon as possible, so the noodles don't have time to get soggy. The problem is that well...its really hot and slurping helps to minimize burning your tongue and lips.
So if you want to complement the chef just do so in person, you can say "gochiso sama deshita" which means "thank you for the meal".
7. Japan is Weird
I'm sure you've seen plenty of YouTube videos of weird Japanese commercials and TV shows with the comments mostly reading "WTF Japan?" There have been plenty of myths about the weird nature of Japan ranging from vending machines dispensing underwear to the doughnut head "fad".
I hate to break it to you but...a lot of these TV shows are either satire or jokes and the people on them are actors. A lot of Japanese prank shows are staged and feature actors, this is also the case for Japanese game shows. You won't find a underwear vending machine on the street corner and a lot "fads" that are discussed in articles aren't really fads.
The truth is that if you find something weird and out of the ordinary then the chances are that a majority of Japanese people think the same way.
The best thing you can do before you travel is to educate yourself about the culture and traditions of the country your visiting to minimize awkward situations.