Copying images is creating ghost folders

You need to define 'copy'. Lightroom Classic does not copy images, and virtual copies are not stored in folders because they are virtual. They only exist in the catalog. But perhaps you mean copies that are created by Denoise, HDR merge, Panorama Merge, and/or editing in Photoshop?

What you describe sounds like the 'Capitalisation problem'. Basically, what happens is that you have two different folders, one called ‘XXXX’ (or a combination of upper- and lower cast) and the other one called ‘xxxx’. In other words, the names are the same, except for the capitalisation of at least one letter. Because MacOS and Windows are case-insensitive, your OS sees those two folders as one and the same folder and so it deals with this without you even being aware of it. You will only see one single folder in the Mac Finder or Windows Explorer!!! But Lightroom is case-sensitive, so Lightroom does see two different folders. Please be aware that this folder is not necessarily the folder you are looking at. It could also be a parent folder (that Lightroom may not show). Here's how to fix the problem. https://www.lightroomqueen.com/capitalization-catalog-error/

Try resetting the preferences of Lightroom Classic:  How to reset Lightroom Classic preferences (adobe.com)

It's recommended to backup your preferences before you reset the preferences to the default settings: 

https://helpx.adobe.com/lightroom-classic/kb/preference-file-and-other-file-locations.html

@liamoconnell 

Please provide a full screen shot that shows the problem.

Creating a Virtual Copy of a photo in LrC cannot create a copy in another folder.