Question

Children of Holocaust: Why were they treated badly? What happened to them?

Answer 1

Scientists used children as lab rats for research, it did not matter that they were children because they came from a Jewish/Traveller family, they were weak and could be taken care of quickly if anything happened. They would also be light and easy to hide from the Nazi public. See to youtube and search for the hangings of lab rat children by nazis for more info

Answer 2

They were treated poorly because of the same reason the Nazi's treated adult jews; it was because of their heritage. After they were sent into camps, it did not matter how old they were, no one was spared of his wrath. 
If you want to know exactly what happened to them with great visuals, I suggest plugging "Children of The Holocaust" into YouTube and finding a great visual explanation to go along with your research.