The officer grins uncomfortably because he recognizes, although he doesn't want to recognize, the darkness of humanity in these "children". They have been warring...evident not only in their face paint and the "sticks with one end sharpened", but the terror in Ralph's face which manifests itself in uncontrollable tears at the relief in being rescued in his eleventh hour. The entire island is on fire and these "British" boys who should be the epitome of well-mannered, civilized, and ordered society are filthy, painted, and hooping like barbarians as they chase Ralph out of the woods.
So, the irony lies in that civilization no longer exists among these boys until the Officer and his crew land on the beach and also in that children are as barbaric and dark as their adult counterparts as far as war, control, and power are concerned.
E-notes defines irony as "a dryly humorous or lightly sarcastic figure of speech in which the literal meaning of a word or statement is the opposite of that intended. In literature, it is the technique of indicating an intention or attitude opposed to what is actually stated."
First of all, it is ironic that the Officer who is fighting in an adult war would question whether the children are at war. Secondly, the boys have been at war, and Ralph has nearly been killed and, of course, both Simon and Piggy have been killed! It is also ironic that the Officer says the boys are all "British boys," and implies as such, they would have good manners, and be raised without the ability to revert to the savagery that war demands, yet we know the boys have easily reverted to savagery and, at the same time, the British adults are engaged in war!