The "mapping relation type" qualifier (P4390) is used (mostly with values skos:exact, skos:broad, skos:narrow) to specify how the original statement is to be interpreted. Example Parkinsons disease:
https://www.wikidata.org/wiki/Q11085

Q11085 --> OMIM ID --> "168600"
                      mapping relation type --> narrow match
Q11085 --> OMIM ID --> "300557"
                      mapping relation type --> narrow match
                    ...

These are not redundant or conflicting values so I don't expect a flag from the single value constraint, but I get one, which is wrong. Especially "narrow match" statements are coming mostly in multiples, but other cases are where one source specifies a qualifier, one not---this is not a contradiction, and should not be flagged.

Best would be with the single value constraint check to simply ignore statements having a "mapping relation type" qualifier.