Updating to 3.9.0 using the one click updater failed to me with the following message:

Matomo encountered an error: Call to undefined method Piwik\Plugin\Manager::getPluginDirectory() (which lead to: Circular dependency detected while trying to resolve entry ‘Piwik\Twig’)

At least one other users had this issue and reported it in the German forum: https://forum.matomo.org/t/update-fehler-matomo-3-9-0/32109

After that broken update, I'm now left with the issue described in #14226. Maybe there is a connection between the two, as both errors/warnings are about the plugin directory.