I noticed that an already closed question was a duplicate (both questions were asked by the same user). I flagged the new newest question of the two, clicked "Other" and typed this:
Duplicate of http://stackoverflow.com/q/<questionID>/<myUserID>
After I submitted the flag, I got the following message:
When flagging a duplicate, please specify the duplicate question (id or link).
Why did I get that error? I included a link to the question right there in the message.
When I changed the message to:
This question is exactly the same as http://stackoverflow.com/q/<questionID>/<myUserID>
I was able to submit the flag just fine.