I am leaving some notes here, in case someone else experiences a similar situation and is being sent here by a search engine. To find out what was going on in a similar case, I ran
on the shell and at least reproducing the same error.
Trying to find out which resource was using it
installing lsof with apt update && apt install -y lsof didn’t yield the expected result. The file was also not accessed anywhere in the host system. What happened?
It turned out there was still a host volume mounted in that directory, so it could not be removed. Taking it out in the docker-compose.yml file helped resolving the update blocker.
May it be that you mounted the logs directory via a Docker volume, too?