RDKit molecule substructure filter

Hi everyone,

I´m using RDKit molecule substructure filter to tag compounds in a list of substances (more than hundreds of substances) from a list of query molecules. My problem: The filter multitags some compounds, which include two or more query molecules substructures but I want only the best matching query tagged. I guess that fingerprint screening treshold may solve this problem, but treshold value variation doesn´t lead to other results.
Does anyone has worked with this fingerprint screening treshold and can fix my problem?

Thanks for help,
Joe