I run an alias to do my updating and it's this:
sudo apt-get update && sudo apt-get upgrade && sudo apt-get autoclean
When the update happens and there is a kernel waiting to be dist-upgraded I 
believe the 
/etc/apt/apt.conf.d/01autoremovekernels file has been manipulated to include 
parts of the wrong kernel
Then when autoclean runs it deletes parts of that kernel rendering it useless.
Thus when a reboot happens, the wrong kernel is wanting to be deleted, again 
triggering 
/etc/kernel/postinst.d/apt-auto-removal and you end up with one kernel.
/etc/kernel/postinst.d/apt-auto-removal should not be triggered as many times 
as it is. As I've mentioned a few
times after rebooting and purging kernels it causes you to have just one.

I took out the autoremove part and if I delete the oldest of the 3 kernels 
before the first reboot, it gets it right.
But, when you reboot before purging the 3rd kernel it will keep on until you 
have one.

** Tags added: xenial

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https://bugs.launchpad.net/bugs/1440608

Title:
  /etc/kernel/postinst.d/apt-auto-removal wants to remove all kernels
  except the latest one

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