Having been in Japan over twenty years I have probably made every single mistake a foreigner can here. There's a reason for that though, Japan just does things differently. Listening to a colleague in his Japanese lesson, the exasperation ion in his question "But why?" Been there, seen it, done it - and feel for him.
If you are thinking of coming to Japan or have just arrived and everything around you doesn't seem to work the way it should, feel free to ask questions in the comments below. It will get easier over time.