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 writing code that clears the duplication votes on b when a is closed as a duplicate of b but historical closures still exist.