Just like
chinti said, Train system in Japan can be confusing since there are 4 types of train sharing the same track! Therefore, it's best to stick to schedule timing (very important) and also take note of the train type mentioned as below.
Local (普通) – stops at every station.
Rapid (快速) – skips some stations.
Express (急行) – skips a lot more stations. The fee for these trains is higher than the local/rapid trains.
Limited Express (特急) – only stops at major stations. Also requires an extra fare.
Your best bet is to stick to only the local and rapid trains (though if you’re riding rapid, make sure the train stops at the station you want to go to). Express and limited express trains can be tricky, though if you are going further out of the metropolitan area (or going into central Tokyo from far away), these might be better options lest you find yourself on the train for 2 plus hours.
When I was first time in Japan, I just simply board any incoming train without checking it properly. So end up 3 stations away from destination point. But it was a good one, since the wrong destination is still quite a place to walk around and explore.

oops i missed out the rapid, i keep thinking something is missing but couldnt think of wat is missing lol.
yea my 1st time i also confused n boarded the wrong train. got panic y the train din stop lol