File Sytem Development Mode - Duplicates in Autogenerated folder

Hi team,

Many times we encounter the error as seen in the below image: 

The above errors are encountered while building workspace in visual studio and also while installing packages. These 'duplications' seems to be coming from auto-generated files.

We have followed the instructions to set up file system development mode as per the documentation. Could you please let us know how to overcome this issue?

Thanks