Right now there's no way of identifying to which group of properties and to which criterion a response belongs to.

This seems to be a need for at least two Stakeholders that are trying to implement the QualificationApplicationResponse. The proposal is to add two new elements to the cac:TenderingCriterionResponse: a cbc:TenderingCriterionID and (ii) a cbc:ParentPropertyGroupID. This way you can refer not only to the group of properties but also to the criterion.