Happens all the time. They had a big surge in these things back in 2005, too.
$1:
This year's jellyfish swarm is one of the worst he has seen, Hamano said.
Meaning he has seen them before. Reasons why he is seeing more of them in Japanese waters than forty years ago are more likely to include the fact that Japanese waters are waaaaaaaaay less polluted than they have been in the past 100 years. The jellyfish probably used to just die before they made it to Japan. Also, add to this the fact that sea turtles (the apex predator of jellies) are threatened and endangered in Asia (turtle soup, anyone?) and it is no wonder they have a population boom in jellies of all types.