New test result:
1. unattended-upgrades is triggered by apt-daily.timer.
yakkety (triggered by apt-daily.timer): Failed
xenial (triggered by apt-daily.timer): Failed
2. unattended-upgrades is triggered by cmdline (sudo unattended-upgrade)
yakkety (triggered by cmdline): Pass
xenial (triggered by cmdline): Failed

This issue can be reproduced on yakkety.

unattended-upgrades received signal, and then it was stopped.
Here is the log:

1. unattended-upgrades.log
2017-06-26 17:30:59,944 INFO Initial blacklisted packages:
2017-06-26 17:30:59,948 INFO Initial whitelisted packages:
2017-06-26 17:30:59,948 INFO Starting unattended upgrades script
2017-06-26 17:30:59,948 INFO Allowed origins are: 
['o=Ubuntu,a=yakkety-security']
2017-06-26 17:33:21,236 INFO Packages that will be upgraded: apparmor 
apparmor-easyprof ...
2017-06-26 17:33:21,236 INFO get_lock returned 174
2017-06-26 17:33:41,569 INFO signal received, will stop
2017-06-26 17:33:41,610 INFO signal received, will stop

2. syslog:
Jun 26 17:33:41 u-Inspiron-5379 systemd[1]: Starting Unattended Upgrades 
Shutdown...

3. unattended-upgrades-shutdown.log
2017-06-26 17:33:41,871 WARNING - Running unattended-upgrades in shutdown mode
2017-06-26 17:33:42,079 WARNING - ps -aef | grep unatteded-upgrade
2017-06-26 17:33:42,316 WARNING - root 2551    1 4 17:33 ? 00:00:00 
/usr/bin/python3 /usr/share/unattended-upgrades/unattended-upgrade-shutdown
2017-06-26 17:33:42,329 WARNING - root 2670 2551 0 17:33 ? 00:00:00 grep 
unattended-upgrade
2017-06-26 17:33:42,345 WARNING - get_lock returned 4
2017-06-26 17:33:42,362 WARNING - lock not taken

** Attachment added: "syslog"
   
https://bugs.launchpad.net/ubuntu/+source/unattended-upgrades/+bug/1690980/+attachment/4903481/+files/syslog

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https://bugs.launchpad.net/bugs/1690980

Title:
  No pop-up window to warn users that system should not reboot or
  shutdown while installing security updates

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