Let us analyze this sentence:
The girl was found in one of the criminals' houses.
There is a group of criminals. At least one of the criminals owns at least 1 house, while the total number of the houses owned in the group is more than 1. Therefore, this group of criminals owns a certain number of houses, in one of which the girl was found.
It's like saying:
This product was created in one of the company's laboratories.
The same way there are many laboratories belonging to 1 entity, "the company", there are many houses belonging to 1 group of people, "the criminals."
Therefore, the sentence is perfectly correct and there isn't really any "more proper" way to express what it says.
Regarding the ambiguity, I wouldn't say it's ambiguous. It simply doesn't specify the number of houses per each person in the group it describes. Therefore it's impossible to determine what number of houses each person owns.
It may be like this:
Criminal 1 owns 3 houses.
Criminal 2 owns 1 house.
Criminal 3 owns 12 houses.
If in one of those houses a girl was found. It really isn't important which person owns how many, therefore the sentence isn't prepared to deal with it in the first place.
Adding another example to back up my case:
I'm interested in buying one of the red houses on Lincoln Street.
Explanation example: There are 30 houses on Lincoln Street. 12 of them have the property of "being red." I want one of those!
I'm interested in buying one of the criminals' houses.
Explanation example: There are 1 000 000 houses in my town. 6 of them have the property of "belonging to a group of criminals responsible for robbing a bank." For some reason I want to buy one of those houses!