Edit: oh - I think that one was actually marked a [dupe] by software. I'd need to double check this, but if so, it's because it interpreted the link to the other thread as a signal of dupiness.
Edit 2: yes, that's what happened. When a submission is heavily flagged and there is a single comment pointing to a different HN thread, the software interprets that as a strong signal of dupiness and puts dupe on the submission. It actually works super well most of the time. In this case it backfired because the comment was arguing the opposite.