Wouldn't the fact that they're 'undocumented' mean we already don't know where they are?
That's what it mean.
They become documented when they enter the USA and go directly into the office at the border crossing facility and apply for asylum. At that point they are legally documented as long as they are awaiting a determination of their application. In these cases, they are held in custody until the hearings. The controversy is about the policy of separating the children from their mothers and preventing communications between those children and mothers.
Critics of the way the government is handling the situation argue that these are refugees who followed the letter of the law when they passed through the manned border crossings and immediately asked for asylum. They argue that the separating of the families is a mean spirited way to punish the families as examples for future refugee families. The cases will probably hinge on "due process" laws in regards to the governments seizing children without due process. Refugees and immigrants are granted Constitutional Rights as soon as they enter USA jurisdiction. Anyone who doesn't except that as the law of the land needs to change a lot of SCOTUS rulings. There is nowhere in the USA where the government can confiscate your children without due process, accept for under Donald Trump's immigration policies and by US Government agencies under his complete and total control and orders.