"We run to those trees, from which the children run away."
Translation:Azokhoz a fákhoz futunk, amelyektől a gyerekek elfutnak.
By separating the verb from the prefix here, you imply that the children are running away from the tree right now. I don't know if present continuous would be absolutely necessary in the English sentence if this is the meaning. If not, then your sentence is correct as well.
Also, "amelyikektől" is actually incorrect in Duo's sentence, it must be "amelyektől", as you wrote.