Question

what happened to Gulliver and his crew members when the Japanese pirate made them what punishment was inflicted on them by the dutchman

Answer 1

When the pirate attacked them, the crew was divided between two ships where as Gulliver was forced to set adrift in the canoe.
This was the punishment, they were ill treated and was being cursed a lot too. 

Answer 2

The two pirate ships were commanded by Japanese captain who spoke little or less Dutch. He interacted with Gulliver and found out that he is a polite person who showed humility, after seeing this the captain decided that Gulliver should not die. Later gulliver told the captain that he felt sorry to find more mercy in heathen than in fellow Christian brothers, this made the captain really angry and he then commanded that Gulliver should also be punished and it should be much worse than death.  it was decided for Gulliver that he should be set adrift in a small canoe and four days' provision. Loading him with all the curses and injurious terms his language could afford.