So I found the solution, and wanted to share it with those that have the same problem.

I went through every primary relationship where the duplications happened (for me it was the male line) I finally found one that had two wives. Each of these wives were linked to the SAME DAUGHTER. The tree determined that EACH of the wives had "Birthed" the daughter and it created multiple links up and down the line.

If you are having duplicate issues that are NOT showing up in the 'people list' (because they are already the same person) then CHECK you RELATIONSHIPS. Odds are that this is the problem.

Thanks for all of your reply's and no, it didn't have to do with cousins marrying each other. like an above poster stated lol.