Nikita, what do you mean by that it does not occur always?

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https://bugs.launchpad.net/bugs/1624644

Title:
  Unable to automatically remove packages that become unused in
  conjunction with updating by other software

Status in unattended-upgrades package in Ubuntu:
  Confirmed

Bug description:
  When using default settings for unattended-upgrades i.e.
  Unattended-Upgrade::Remove-Unused-Dependencies "false"; 
  # default "false"
  Unattended-Upgrade::Remove-New-Unused-Dependencies "true"; 
  # default "true"
  in configuration file /etc/apt/apt.conf.d/50unattended-upgrades,
  U-U is unable to remove packages that become unused in conjunction with 
updating by other software such as update-manager or apt full-upgrade. This is 
because U-U compares the list of unneeded packages before and after it upgrades 
packages to detect which packages are new unused ones.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: unattended-upgrades 0.90
  ProcVersionSignature: Ubuntu 4.4.0-36.55-generic 4.4.16
  Uname: Linux 4.4.0-36-generic i686
  ApportVersion: 2.20.1-0ubuntu2.1
  Architecture: i386
  CurrentDesktop: XFCE
  Date: Sat Sep 17 11:28:44 2016
  InstallationDate: Installed on 2016-09-05 (11 days ago)
  InstallationMedia: Mythbuntu 16.04.1 LTS "Xenial Xerus" - Release i386 
(20160719)
  PackageArchitecture: all
  SourcePackage: unattended-upgrades
  UpgradeStatus: No upgrade log present (probably fresh install)

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