Why is an extra copy of the file created when I upload files to Apple Files?

How is OneDrive configured?

It sounds like you're trying to sync multiple devices to the same OneDrive account, in addition, those devices are also synching via iCloud Files, in which case it sounds like you have a race condition...

On Device 1 (let's say this is the iPad), you save a File to iCloud Files

iOS uploads the file.

While it's being uploaded, OneDrive kicks in and copies the file

While OneDrive is uploading the file, iCloud synching kicks in and the second device (say, the iPhone) sees the file.

OneDrive on the iPhone now sees the file and starts to synch it... but! uh oh! there's already another file there with that name, so let's create a duplicate.

It's only speculation, and it requires a specific set of circumstances (multiple devices synching to both iCloud and OneDrive at the same time), but its about all I can think of off-hand.

The solution? Don't have OneDrive synch your entire device. I don't use OneDrive, so I don't know how to tell it to do that.