The myth is that the cost of living in Japan is ridiculously high and that apples cost the equivalent of 50 USD each. If you did fancy buying a 50 USD apple then there are places which do indeed sell em at that price. But the fact is that most media are not going to cover stories of apples that are reasonably priced.
If however you are hearing from a friend that their trip to Japan cost a bomb then its probably because they were spending time in a hotel and eating at out all the time at touristy places.