There is a bug in ./libraries/src/Installer/InstallerAdapter.php method protected function setupScriptfile()

when you have eg. the following updates in the Joomla update manager:

1. a plugin with < scriptfile> in manifest that triggeres a preflight which removes a directory
2. a package which doesn't have < scriptfile>, but has a component with a < scriptfile>

the plugin installs correct and the directory is removed (and filled again with the correct files in the updated file)
but the package installs and executes the plugins preflight agian... leaving the plugin installation in a flux as the directory is removed again.

Debugging led me to the following bug in protected function setupScriptfile()

    // When no script file, do nothing
    if (!$manifestScript) {
        return;
    }

this just returns, but the script class for the plugin is still set in $this->parent->manifestClass and as such the preflight is executed.

this is the (confirmed fix) that avoids the 'bleeding' of the plugins scriptfile to the package:

    // When no script file, reset any previously set manifestClass and do nothing
    if (!$manifestScript) {
        $this->parent->manifestClass = null;
        return;
    }

hope this helps, keep up the good work!