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:
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.