I've been having these problems, too. In one case, I tried to install ubuntu-restricted-extras, and the operation got to the point where I had to manually choose 'yes'. to accept a EULA license, but there was no apparent way to accept it and the package just stayed stuck forever.
The solution above seemed promising, but when I got to su 32011, the response was No passwd entry for user '32011'.
Moving forward, I think i'm going to either run:
libertine-container-manager install-package -p PACKAGE-NAME
or, I'll run
libertine-container-manager exec -i CONTAINER-IDENTIFIER -c "COMMAND-LINE"
and once in here, I'll just run apt install PACKAGE-NAME. It feels more natural, to me, to get into the libertine shell and run apt commands, but I don't know if there's any benefit to the other method. I don't know that packages installed with apt are going to show in up the libertine GUI, but at this point, I'm going to try to avoid that GUI as much as possible. It's just not a viable way to install packages, if there's a chance the installation process will prompt the user, and there's no way to interact with the operation.