Phusion Passenger: what causes "Cleaning stale instance...Directory not empty" message when using passenger-config or passenger-status

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It seems everytime I restart my Rails 6.0 application using passenger-config restart-app /path/to/app, I get a warning that there are stale instances, like so:

*** Cleaning stale instance directory /home/user/rails_apps/passenger-instreg/passenger.gJHicfi
    Warning: Directory not empty @ dir_s_rmdir - /home/user/rails_apps/passenger-instreg/passenger.gJHicfi

I did configure a specific PassengerInstanceRegistryDir in the Apache module configuration, as well as defined the PASSENGER_INSTANCE_REGISTRY_DIR env variable, but still, my user (under which I run the passenger utilities) does not seem have the correct permissions to remove the stale directories.

How do I avoid this?

I run Passenger 6.0.6 on Red Hat Enterprise Linux release 8.2 (Ootpa), with Ruby 2.7.1 installed via rbenv.

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