The way this happened in the past was that 

 - question a and question b got various votes as duplicates of each other.
 - question a is closed as a duplicate of b
 - question b is closed for some non-duplicate reason
 - the majority votes on b are for duplication and the majority action counts

This edge case was [solved by the stack developers](http://meta.stackexchange.com/questions/263331/circular-duplicates-strike-again) writing code that clears the duplication votes on b when a is closed as a duplicate of b but historical closures still exist.