The short answer is that they were only put into isolation when the disease started. Prior to this, they were presumably able to freely mingle with the crew of the USS Lantree, including the officer who had the flu.
KINGSLEY: But the children have been in protective isolation since this was detected. They show no symptoms. You cannot leave them here to die!
Episode Transcript - "TNG: Unnatural Selection"
Interestingly, the line in the original show script was slightly different, albeit it makes the same point about the children only being placed into isolation after the disease took hold:
We have thirty-two children here.
They've been kept in positive
isolation since the onset, and
so far they've shown no symptoms.
You must evacuate them as soon