I suspect there is nothing the git project can do about it. Windows refuses to delete files which are open, and many different applications (virus scanners, malware detectors, other file system connected programs) can leave files open while git rapidly traverses the file system to remove files.
The git client plugin 1.19.1 is slated to include a silent, single retry of git clean on Windows, in case an immediate second attempt is successful. I don't hold much hope for that either, but it is an attempt and is nearly harmless to the plugin to attempt a second clean if the first throws an exception.
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