I added more debug messages (ps -aef | grep unatteded-upgrade) to 
unattended-upgrades-shutdown.
In xenial, it looks like unattended-upgrade is killed before 
unattended-upgrades-shutdown is running.
That is why unattended-upgrades-shutdown can get lock.

Log:
1. xenial (unattended-upgrades-0.90ubuntu0.6):
unattended-upgrades-shutdown.log
2017-06-23 15:27:09,824
WARNING - Running unattended-upgrades in shutdown mode
WARNING - ps -aef | grep unatteded-upgrade
WARNING - root     16581     1  0 15:27 ?        00:00:00 /usr/bin/python3 
/usr/share/unattended-upgrades/unattended-upgrade-shutdown
WARNING - root     16662 16581  0 15:27 ?        00:00:00 grep 
unattended-upgrade
WARNING - get_lock returned 4
WARNING - lock not taken

2. yakkety (unattended-upgrades-0.92ubuntu1.5):
unattended-upgrades-shutdown.log
2017-06-23 13:52:55,720
WARNING - Running unattended-upgrades in shutdown mode
WARNING - ps -aef | grep unatteded-upgrade
WARNING - root      5193  1298  0 13:49 ?        00:00:00 sudo 
unattended-upgrade 
WARNING - root      5196  5193 61 13:49 ?        00:02:14 /usr/bin/python3 
/usr/bin/unattended-upgrade
WARNING - root      5379     1  0 13:52 ?        00:00:00 /usr/bin/python3 
/usr/share/unattended-upgrades/unattended-upgrade-shutdown
WARNING - root      5444  5379  0 13:52 ?        00:00:00 grep 
unattended-upgrade 
WARNING - get_lock returned -1
WARNING - Unattended-upgrade in progress during shutdown, sleeping for 5s
...
WARNING - get_lock returned -1
WARNING - Unattended-upgrade in progress during shutdown, sleeping for 5s
WARNING - get_lock returned 4
WARNING - lock not taken
INFO - All upgrades installed

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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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