I'm doing this from Memory since I haven't played NCAA since I got Madden. I think the Difference I may have made was that I did NOT talk anyone into staying. TEST: Try this out. Save your Fanchise just before Advancing into the Off Season (After the last Bowl Game is Played).
Enter the new season and go to Players Leaving. Don't talk anyone into staying and continue to Export and then CPU removes the players. Sim the rest of the Off Season and Sim an Entire Yr. Jump to Offseason and go to players Leaving. Export and continue where CPU removes the players. You should have 2 draft classses.
Now jump over to Madden and Sim an Franchise Yr. Go to Off Season and check your 1st draft class. Make notes of the top names. Sim another Yr and load the 2nd draft class. If you still see the same guys popping up Twice, then I'm sorry I don't know what else to tell you.
That's what I did in my Franchise. I had 2 save classes that Had a bunch of Repeats. I went and Simmed 2 straight draft classes and save each. Jumped back to Madden and Loaded each draft class and did Not get any Duped players when I did it.
I hope it works out, otherwise I know of no other way around it.