It is the apt-daily-upgrade.service called with the apt-daily-upgrade.timer every day. I don't know why it make problems on your installation. Anyway, you don't want to run it automatically. You can disable the timer with:
rpi ~$ sudo systemctl disable apt-daily-upgrade.timer
The problem is that you can't do it because the boot get stuck on executing the service. When looking at the service with:
rpi ~$ systemctl cat apt-daily-upgrade.service
# /lib/systemd/system/apt-daily-upgrade.service
[Unit]
Description=Daily apt upgrade and clean activities
Documentation=man:apt(8)
ConditionACPower=true
After=apt-daily.service network.target network-online.target systemd-networkd.service NetworkManager.service connman.service
[Service]
Type=oneshot
ExecStartPre=-/usr/lib/apt/apt-helper wait-online
ExecStart=/usr/lib/apt/apt.systemd.daily install
KillMode=process
TimeoutStopSec=900
you see that the service will timeout (TimeoutStopSec) after 900 seconds, that are 15 minutes. So boot your RasPi and wait at least 15 min. Maybe the RasPi will continue booting and you are able to disable the timer.