At most Japanese drinking establishments, one pays by the hour, not by the drink, and a cover charge is often included. Beer, juice and soda are also normally available. These are not normally free, but you will get them and pay for them whether you want them or not. In fact, these items are often quite expensive, and that is one of the ways bar owners make their money. That is the system.
Japanese patrons know it and accept it.
You won't be able to change, it so just view it as part of the cultural experience. Some snacks are very expensive and it is difficult to discern a bar's pricing system simply by looking inside the bar. Again, ask about the price before you sit down. Most places will gladly inform you of the cost and will not try to take advantage of you with hidden charges. It is a good idea whenever possible to go out with your Japanese friends and counterparts.