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Duplicates get there because you enter them, plain and simple. You may enter them by manually adding them, or they may get added when you are doing a merge of data found during a web search. When family names are available to add during the merge, FTM will ask you if you want to merge with an existing individual, add as a new individual, or ignore. You may be selecting add instead of merging with an existing individual. I think this is the most likely way they are getting added. Just watch carefully when doing your merges so that you select the proper action.
Hope this helps. Good luck.