Public bug reported:

I get ubuntu notification that I have update and this notifications is
very annoying, but I run update manager and get than my system is up to
date but
sudo apt update 
Hit:1 http://by.archive.ubuntu.com/ubuntu xenial InRelease
Hit:2 http://by.archive.ubuntu.com/ubuntu xenial-updates InRelease             
Get:3 http://by.archive.ubuntu.com/ubuntu xenial-backports InRelease [92,2 kB] 
Hit:4 http://archive.canonical.com/ubuntu xenial InRelease                     
Ign:5 http://dl.google.com/linux/chrome/deb stable InRelease                   
Hit:6 http://dl.google.com/linux/chrome/deb stable Release                     
Get:7 http://security.ubuntu.com/ubuntu xenial-security InRelease [94,5 kB]
Fetched 187 kB in 0s (255 kB/s)                                
Reading package lists... Done
Building dependency tree       
Reading state information... Done
3 packages can be upgraded. Run 'apt list --upgradable' to see them.
W: http://dl.google.com/linux/chrome/deb/dists/stable/Release.gpg: Signature by 
key 4CCA1EAF950CEE4AB83976DCA040830F7FAC5991 uses weak digest algorithm (SHA1)
W: http://dl.google.com/linux/chrome/deb/dists/stable/Release.gpg: Signature by 
key 3B068FB4789ABE4AEFA3BB491397BC53640DB551 uses weak digest algorithm (SHA1)

apt list --upgradable
Listing... Done
lshw/xenial-updates 02.17-1.1ubuntu3.1 amd64 [upgradable from: 02.17-1.1ubuntu3]
mplayer/xenial-updates 2:1.2.1-1ubuntu1 amd64 [upgradable from: 2:1.2.1-1]
mtr-tiny/xenial-updates 0.86-1ubuntu0.1 amd64 [upgradable from: 0.86-1]

Run update manager again and "my system is up to date"

update manager has inconsistent state

ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: update-manager 1:16.04.3
ProcVersionSignature: Ubuntu 4.4.0-24.43-generic 4.4.10
Uname: Linux 4.4.0-24-generic x86_64
ApportVersion: 2.20.1-0ubuntu2.1
Architecture: amd64
CurrentDesktop: Unity
Date: Fri Jun 10 16:35:09 2016
GsettingsChanges:
 b'com.ubuntu.update-manager' b'window-height' b'456'
 b'com.ubuntu.update-manager' b'first-run' b'false'
 b'com.ubuntu.update-manager' b'window-width' b'1035'
 b'com.ubuntu.update-manager' b'launch-time' b'1465565684'
InstallationDate: Installed on 2016-05-12 (28 days ago)
InstallationMedia: Ubuntu 16.04 LTS "Xenial Xerus" - Release amd64 (20160420.1)
PackageArchitecture: all
SourcePackage: update-manager
UpgradeStatus: No upgrade log present (probably fresh install)

** Affects: update-manager (Ubuntu)
     Importance: Undecided
         Status: New


** Tags: amd64 apport-bug xenial

** Attachment added: "Screenshot from 2016-06-10 16-42-45.png"
   
https://bugs.launchpad.net/bugs/1591214/+attachment/4681076/+files/Screenshot%20from%202016-06-10%2016-42-45.png

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https://bugs.launchpad.net/bugs/1591214

Title:
  Update manager has no update when apt has

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