Japan is a very peaceful country, and disputes are usually handled in a very professional and calm manner. To become angry and explode on someone else is considered very rude and unprofessional, so you don’t see bosses or subordinates having full-blown fights often.
Disputes are not common in the first place as Japan is a country of conformity. They will avoid fights at all costs to protect the group and go with the flow. If there is an issue, such as a huge mistake has been made, it should not be fought or argued. My experience is that if you make a mistake, your best option is to apologize and say that you will be careful not to make the same mistake in the future. You will eventually get reprimanded for something that you do by your bosses, but talking back is not the way to go, and talking back can start a bigger fight than the original blunder is worth. It ruins your reputation and people lose respect for you if you do so.
Disputes involving the law should be handled similarly. If you get caught speeding or riding your bicycle at night without a light, the best thing is to apologize for your mistake, and not make excuses for as to why you could not uphold the law. You’re more likely to get off with just a warning that way. The same is true for altercations with other people on the streets. If a minor offense has been committed and you know that you are not at fault, the best thing to do is remain calm until the police come, and avoid becoming aggressive. The police will usually side with native locals, so being as objective as possible is the best way to get justice.
Never try to argue with someone, especially if they are your superior. If you find something wrong with a policy or system, I advise approaching the topic in a friendly and suggestive manner. It may take time for change to happen, and it can be frustrating to feel as if your voice is not being heard, but persevere, and the benefits will show themselves eventually.