To me, this sounds like a syncing issue with Google drive.
The major problem with Google Drive is that Google Drive does not use a "normal" hierarchical file system:
File in google drive can have multiple "parents" and, what causes the biggest issues when syncing to hierarchical file systems like OSX or Windows, folders can have files with identical names.
That means that the Google Drive sync client has to "enumerate" identical named files on the client computer, and this sometimes breaks the association to the files in the cloud (especially when applications alter these files using temporary backups). If this association is lost, the client uploads a "new" and identically named file to the cloud, what results in duplicate files.
A workaround could be to close the Google Drive client during work and only start it for syncing afterwards. To handle existing duplicates, check the Google Drive website and delete the oldest version duplicated files.