Usually when trains are delayed it's due to one of two reasons:
Some kind of mechanical failure. Even if the failure itself had nothing to do with the train you're catching, it might cause your train to get stuck in a queue while the issue with the stricken train is resolved. This risk can be mitigated by proactively investing in the infrastructure so that your hardware isn't as old and worn down and prone to failure. That's something that a lot of countries don't do a very good job across both the public and private sectors.
An issue with an actual passenger. So if you've got an unruly passenger or someone has some kind of health issue, it can cause a train to be held up. Again, it doesn't necessarily need to take place on the train you're catching because there can be a knock-on effect. Some countries are more procedural and strict than others in how they handle these types of issues. There may be certain issues that would hold a train up by an hour in the UK, but only a few minutes in Japan due to the protocol being applied.
Additionally it helps that a lot of the busier areas of Japan's rail infrastructure have contingency built in. So if a train gets stuck for whatever reason there's more capacity for other trains to go around it rather than being stuck behind it.