I've reproduced the issue once again and I believe I've found the culprit. When downloading a file for the first time in Vandium's incognito mode you will receive a popup similar to the following (i am paraphrasing), "Downloads in incognito mode will be visible to other users on this device, proceed?" This prompt will come with a button to continue the download.
The ghost files are spawned when the following conditions are met:
- The user attempts a download for the first time in incognito mode
- the prompt listed above appears
- The user does not click accept/download instead attempting to reinit the file download process.
This will create a second entry in androids storage indexer and unlink the first entry from chromium's download manager, in turn creating the ghost file.
The only solution to this is A. disable the prompt using a patch or B. file the bug upstream. I don't know much about aosp so I encourage anyone who knows how to report a bug to google to attempt to reproduce this in a user profile. Hope this helps.