The absolute biggest one is lying to your face :-) In Japan, it is really impolite to be overly critical of people or to act in an unfriendly manner. Everybody you meet will be nice to you and if you say, "I like underwater basket weaving" they will say, "Oh yes. That is very interesting" and smile. If you unintentionally force them into a confrontation like by saying, "Do you really think it is interesting? Do you like underwater basket weaving too", they will say, "Oh yes. I like underwater basket weaving" just to escape the conversation.
One of the side effects of this is that people can be super friendly to you, but you never really know if they like you or not. I have an ex colleague who was very helpful to me when I moved here. He looked out for me and even invited me to his home for dinner many, many times. He hooked me up with local groups, etc, etc. He even occasionally still asks me to go to some local events these days. But I'm pretty sure he hates my guts. He doesn't even send me a new years card even though I send him one (which seems like a pretty weird criteria for judging if someone likes you or not, but...)
You just don't know. People will never tell you outright stuff like this and they will "lead you on". Virtually every expat I've known who has problems in Japan loves to jump on this issue. "People here are false", they will say. "You can't trust them. They will lie to your face." There is a concept called "tatemae" which is the face that you have to present to society and it's a concept that rubs many westerners completely the wrong way.
Personally, I like it. I don't care one iota if my ex colleague likes me or not. He's been incredibly helpful to me. He treats me really well. He's been nothing other than a massive positive force in my life. Yeah, it's a shame we can't be friends, but that's life. Everybody treats me well here. Everybody is friendly. Everybody is nice to each other and treats you as if you are a friend, even if they don't know you -- even if they hate you.
But... yeah... it takes some getting used to and some people really don't like it.