There are many instances of irony, but the primary one is that the fire which Jack and his followers started to kill Ralph ended up being the signal that the rescuer saw to come and save him. Ralph had been considering and trying fire signals which are a sign of the history of humanity (building a fire) to attract attention from rescuers, but by this time the island had lost its sense of civilization. Hence, its quite ironic that the symbol of it, fire, was ultimately the resource used on their behalf, especially a fire built to kill.
Secondly, the naval officer which came to the rescue was himself a man of war and conflict as he was military, yet, he saw that these uncivilized and wild children were nearly inhumane- Yet, the irony is: Isn't the carnage of war inhumane as well?
Finally, the ending was not a happy one. You would have thought that the children would cheer and jump up and down. Nope. They were just astonished because they had become ultra-removed from the normal world. This man was basically interrupting the world as they now knew it, not rescuing them from it. Ralph fell apart, the kids were shocked, the man was disgusted. This was ironic in a story where you wish at all moments that they get rescued and you would think this would be a moment of joy. It is also then when you realize that, for these kids, life would never be good, healthy, or ever the same.