Tente definir DEBIAN_FRONTEND como não interativo. por exemplo,
export DEBIAN_FRONTEND=noninteractive
apt-get update && apt-get upgrade -y
Veja man 7 debconf
para mais detalhes:
noninteractive
This is the anti-frontend. It never interacts with you at all, and makes the default answers be used for all questions. It might mail error messages to root, but that's it; otherwise it is completely silent and unobtrusive, a perfect frontend for automatic installs.
If you are using this front-end, and require non-default answers to questions, you will need to preseed the debconf database; see the section below on Unattended Package Installation for more details.