It sometimes happens that a question has more than one problem, and could be closed for all of those. When that happens, the reason that collected most votes is chosen as the close reason: there can only be one close reason.
As noted in the answer, several close reasons would not be helpful, and actually confusing. However, I find the cases 1, 4 and 5 of this answer less "confusing" than "hypocritical" (note that the available close reasons have since changed): if the question is deemed a duplicate, how can it be unwanted for another reason? Why wasn't the other question unwanted too?
As I understand it (for example from this post), closing a question as a duplicate is like pointing the OP to another place with his answer, and adding a big flashy sign:
Dear visitor from the future,
If you have the same problem as this question, it is likely that you will find your answers in this other question.
If a question is voted a duplicate by at most 2 out of 5 voters, this information is lost. Is there good reason for this? The question is not deleted, after all, so some future visitors could still land there.
Or is it a problem on bigger sites, where real unsalvageable garbage questions exist? On smaller sites, I know of at least one instance where this behavior has indirectly caused confusion.
My suggestion would be to have the duplicate shown somewhere, regardless of the close reason. Either by adding
This question may have already an answer here: ...
on top of the question anyway, or by building a custom message for this kind of twin reasons, making the duplicate stand out.
An additional benefit would be to encourage reviewers to look for a duplicate when they see a question with 3 "off-topic" close votes for a question they would vote as duplicate (which would be useless today).
A longer-term solution could be to completely separate the two voting queues, one for duplicates, one for real closing reasons. (Rationale: closed questions are all fundamentally unwanted, except for duplicates.) This would allow for additional features, for example marking an already closed question as duplicate (this guy would thank us), or giving the OP a binding vote on duplicate votes.