More details on the story would really help, but...
So a lot of people have suggested that they are children of the separatists, but I don't see it. If you want to kidnap the children for leverage you keep them somewhere safe. If you are just doing it as a "ha ha" type of punishment, then just kill them or dispose of them in space.
Things that I can see working:
The whole thing was accidental. Someone in this large government misfiled some paperwork. The government officials aren't even sure if they did kidnap any children or if its just the separatist trying to create a media scandal. Some officials are trying their hardest to get the children back, but no one knows where they were sent because the documentation was misplaced. Or maybe its malicious bureaucracy. The government did it, but noone involved really knows why, even the decision makers. (If you watch the movie CUBE, this is hypothesized as why the Cube exists. The government built a death trap and then asked, "Why did we build this? I guess we should put people in it."
There was some valid purpose to sending these children, but there were supposed to be adults. A cryo-failure resulted in everyone over 75 kg, all of the adults, dying. Or perhaps a power failure to lifesupport made the crew make a tough call. They sacrificed themselves so there would be enough juice for the children to survive.
Other people have said this, but it seems like a decent answer.
This season on, "will your child survive?" Extreme reality TV, the next hunger games, ect.
Maybe this is a hell planet (haven't told us a lot) and the point is that the strongest of them will survive and be strong survivors. Who ever lives is going to then be trained as a soldier.
Or perhaps all of these children have latent psych powers. They must be put into extreme or stressful situations to awaken them. However being around normal humans will dampen their ability to discover their powers.
These children have something wrong them. Something REALLY wrong with them that cannot be quarantined in a normal way and the government doesn't really want people to know about. Some strain on nanomachines and they are worried about a gray goo scenario. There was some debate about just nuking them from orbit, but some people felt this would be morally wrong.
Or perhaps they have a psychic virus. There is no known way to contain it, only to isolate it. The government plans to observe them to learn more.
Unbeknownst to the rest of humanity, the government has secretly been contacted by a powerful extraterrestrial empire. These aliens have demanded a tribute. The government, knowing that it will not survive a war is forced to comply.
Its not just these 100 children. The government has developed means to rapidly transport people but knows it is facing some existential crisis. They are transporting as many people as quickly as they can to habitable worlds outside their borders (or even in other dimensions / times). It is pure chance that these 100 children ended up by themselves on this planet.
The government has discovered time travel and also that there is a self fulfilling paradox. This planet is actually prehistoric Earth, and those children are the first humans.