We started having this same problem on our WS 2016 Domain Controller.
It normally takes 20minutes to backup this server, but last night it hit runtime limit of 4hours and the cause was tracked down to be over 200k new files in C:\ProgramData\Microsoft\Windows Defender\Scans\History\Store.
It looks to be the system process that is creating these random 1KB to 2KB files in said locate, this is an assumption as the owner of the files is System and in Ressource Monitor>Disk I can see the System process accessing said folder location.
Since 22:11 last night it has been creating hundreds of thousands of these files and it continues to do so after a reboot.
Windows Defender GUI isn't running a scan, doesn't show anything in History.
Windows Defender Operations log in EventViewer does indicate why these random files are being created.
What is the C:\ProgramData\Microsoft\Windows Defender\Scans\History\Store\ folder for?
How do I determine what is constantly creating these files?