Generally this is not allowed by the API. It may be a result of a bug somewhere. Could you please provide some more information:
1) What exact API calls are you making? Create folder only, or are you performing copies or moves? Is your folder creation part of folder templates? 2) Do the accounts seeing this issue have versioning turned on? 3) In the picture above, is that a shared folder or a personal folder containing the duplicates?
Thank you in advance. I will continue research to see if I can find anything in the meantime.