The first step in resolving this is to check Planning Center to make sure that there are no duplicates there. Planning Center has a duplicates detector on the main page of People. After assuring that there no duplicates and they still persist to show in the directory, check households. If a directory is grouped by household, folks that are in multiple households will be shown in each household. You can change households on Planning Center to correctly place your folks in the right households.
Planning Center's help on households can assist you through this: https://pcopeople.zendesk.com/hc/en-us/articles/360000371668-Edit-Profile-Information#households