Something that travelers should be aware of is the "otoshi" seating charge system. There is no tipping in Japan; sometimes there is a service charge on some hotels or a few services. However, almost all resturants and bars (excluding fastfood, cafes, and family style restaurants) have a seating charge. When you sit at a restaurant, you will be given a small plate or bowl of food. It can be rice, fish, meat, salad, anything really. Most of the time it is a set food item that you don't choose. It can change daily. This is not free and you will be charged for it. Otoshi generally cost between 300 and 600 yen. So you should factor this in if eating out. You cannot refuse this charge, but you don't have to eat what you are given.
Before coming to Japan, I would highly recommend booking a portable wifi device (or pocket wifi) in advance or at the airport. Average rental price is about 900yen/day. It can usually be picked up at the airport or delivered to your hotel. You'll find it to be very convenient to have instant connection to things like Google Maps, Google Translate, Hyperdia, JapanTravel.com, etc. Locating wifi hotspots may be difficult (and slow) depending on where you are.
The language barrier can be an issue, and you might find yourself getting lost quite a bit if you don't have a map or access to Google maps. Stations like Shinjuku are huge with many different entrances and you have to take note of which line you are taking to get to the right platform. If you don't speak Japanese, finding a English-speaking local to ask for directions isn't easy.
A problem I had was not getting the exact address and simply relying on Google Maps. Google Maps works perfectly about 90% of the time in Japan, but there are still some glitches. I looked up the Ramen Museum in Yokohama, but ended up a few stations away apparently where the old spot was?
Another problem I have had was having to walk from JR stations to different lines or Subway stations. This is a huge thing to watch out for if you don't have data or can't use your phone. I got mixed up a few times because of this. Re-check your travel plans before you go!
The usual problem I encountered were young train attendants working at the stations. I have encountered many rude and impolite (mostly young) staff already. When you don't speak Japanese, they do not give you the service you deserve and they never answer you directly. In a society where politeness is practiced, it gets really frustrating to meet young people who are like this.
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