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After apt update and apt upgrade all except one docker container aren't started anymore.

Containers have status exited using docker ps -a and can be started using docker run $containerid

Where should I start fixing?

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At first you shouldn't use docker run for existing containers but docker start

From the official documentation :

docker run

Run a command in a new container

docker start

Start one or more stopped (includes exits) containers

For your issue, I suggest you to recreate (so with docker run) your container with the flag --restart always Source and more info

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    I would also mention restarting the docker daemon for containers running in the background e.g., via -d.
    – oxr463
    Commented Dec 11, 2020 at 20:53

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