Entering the US illegally (the first time) is a misdemeanor, which is a pretty small thing, so previously that wasn't considered a good enough reason to separate families. They were mostly referred to civil deportation proceedings instead of being criminally charged. Entering the US to apply for asylum isn't illegal, but it seems at least some have been charged and their children taken anyway. e.g. https://twitter.com/PeterWelch/status/1008443579876958208