Grades In Ladder Table and Mapping Table Relation

So I want to assign SourceSystemId to existing Progression Grade Ladders and all of the child objects of Progression Grade Ladders. I managed to assign almost all of the records but I encountered issues in GradesInLadders object. To my knowledge, SourceSystemId is automatically provided if we didn't assign one and it was always the SurrogateId which is also the Id for the object i.e (GradeId, GradeLadderId, RateId). Now what I wouldn't understand is on GradesInLadderId I have some records on our environment on which the SurrogateId on the mapping table doesn't match the GradesInLadderId. When I did a query on