Could the issue be related to a config by unattended upgrades

Whether or not unattended-upgrades will perform the cleanup (auto remove) is 
controlled by the Unattended-Upgrade::Remove-Unused-Dependencies setting in 
/etc/apt/apt.conf.d/50unattended-upgrades. Set it as follows to enable the 
cleanup -- and you should be able to remove the explicit autoremove cron-job:

Unattended-Upgrade::Remove-Unused-Dependencies  "true";

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  boot partition full

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