I had this happen, I just had everyone ignore the duplicate player and everything seemed to be in order. Then mysteriously in the next draft the players in question showed back up in the draft pool (Most likely because they weren't signed). Marcus did fix my file and labeled it "slightly corrupt" But looking back at the issue the double import is most likely the cause of my issues the next year with the draft.
Here is the thread that pertains to the issue (It won't help you now, but we have an idea of what probably caused it)
http://www.ootpdevelopments.com/boar...eat-issue.html