You shouldn't add duplicate folders to the synchronization process. For example, never add a folder that's accessed by two applications. Secondly, you need to make sure that only one application is allowed to sync files.
1 - App1
2 - App2
3 - Sync Folder
1 - 3 - 2 (App1 - Sync Folder - App2)
As you can see, the sync folder will be accessed by two applications/sources, and when this happens you will have synchronization problems. It's called a synchronization loop, because each app will continuously sync due to the changes being made. The fix consists in using separate directories for each sync operation rather than using just one where all the files will be stored.