Thanks to Kyle for pointing me in the right direction. I found that there were multiple XML files in my ArcGIS/My Survey Designs folder that was the cause of the duplicates. These xml files were named the same as the surveys but were under different survey folders. I deleted them and then restarted connect and the duplicated surveys were gone.
Renaming the extension on survey named xml file within each survey should allow someone to keep all of the files for a survey but not have it show up in connect. I've tested this to work for me.
