This is because nearly all of the language education focuses on rote memorization, and oftentimes students who go 'outside the box' and learn to speak properly are punished.
My fiancee, a Japanese national, was bullied in high school for her 'weird' English... because she was the only student in the entire school who took advantage of the American teacher provided through the JET program.
Friendships are the second problem. Japan is a country where your friends are dictated by and large through group affiliation, although that's slowly changing. Making friends by talking to, say, the stranger next to you at a Starbucks is pretty unthinkable.
Third is arrogance; the idea of 'when in rome...' doesn't seem to exist here.
For example, I once had a group of Japanese 'friends' insist that it was totally okay to be amazingly rude by American standards, because their actions were fine by Japanese standards. Things like making plans and then never showing up, 'forgetting' to pay for their fair share of the beer, etc.
Fine logic, except we all happened to live in California at the time. Needless to say, I don't associate with these people anymore, but it's worth noting that few of them stayed in the country, and that even the two that kept on in the U.S. spend all their time with 'Japanese' friends, and have made zero effort to really integrate into the local culture.