Windows locks directories entirely after I try deleting them

I have a problem where sometimes Windows blocks access to a directory entirely (and I mean entirely; I can't even see the owner, file permissions and other metadata). The problem is not entirely reproducible but happens especially when I switch Git branches in a large source code repository. It can also happen elsewhere, such as when I delete a large number of directories using a script.

I have verified that the directory is not in use by a running process (using Process Hacker/Process Explorer), and I tried to reset ownership of the directory without success (In fact, Windows Explorer can't even display the owner).

The only thing that solves the problem is a full system reboot, after which the directory is either available again or removed (not sure what determines this).

The first time it happened I didn't think much about it, but now it has happened at least 10-20 times, on two different machines (both running Windows 10).

When the directory is locked, I tried killing all user processes and stopping the antivirus software, but it did not help. From what I can tell, this is not a case of the directory being used by some process. I suspect that the directory is locked by the keel or NTFS driver itself for some reason, and I could not see any way to unlock it from user space.

I am curious why this happens. Is this a bug or expected behavior (some kind of security feature maybe)? Corrupt filesystem? I did not see this in earlier Windows versions.

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