This has been reported a long time ago; things might very well have been fixed by now. I can hardly imagine this is a real issue, but maybe it's not too nice for SEO or the data dump? So:
A question on Super User had its comments about duplicates removed by a moderator. However, the "Linked" section still showed the links for many months, until somebody edited an answer:
Jeff writes that links are cleaned up every 30 days, or whenever a post is edited. The first was not true for this example: the links were definitely still there almost 4 months later (on May 4th 2011). Looking again in October showed the links were okay, but at that time the post had been edited.
I think one link was still used in the 4 close votes that had not expired yet. The other was a link to another duplicate, which might only have been in the comments, not in any vote. (As I voted, I only see "You have already voted to close this question" so cannot validate which duplicates were used. Both links were in my comments.)
This is related to Posts linked in deleted answers still show up under “Linked”, which meanwhile has been tagged
status-bydesign. But while 10k can see deleted answers, deleted comments cannot been seen by anyone but moderatos.