Sorry for my late reply. As I have found from other threads, I think I have an idea why this is happening:
The directories that have been duplicated are usually the ones with Google Docs or something similar inside. Currently, I am having a dual boot system (Win10 & Ubuntu) on my machine and in order to save space, I am sharing the same Google Drive directory for both systems. I think this might be the reason why folders and files keep being duplicated, with most being Google Docs or similar files. I refer to the following thread: .gddoc files have appeared in my drive