The issue is that you used the GNOME3 Staging PPA for Xenial. As soon as
yakkety opened up, you upgraded to yakkety keeping the GNOME 3.20
packages but without the GNOME3 PPAs.

The PPA has a note that you should run ppa-purge prior to upgrading to a new 
Ubuntu version:
https://launchpad.net/~gnome3-team/+archive/ubuntu/gnome3-staging/

The systemd file was moved in this version. I didn't notice at the time that 
the PPA had installed the file in a different package than Debian did.
evolution-data-server - 3.20.3-1ubuntu1~xenial1         jbicha  2016-06-07

Had this issue been reported sooner (like in June), I would have added a
Breaks/Replaces for the move. By now, nearly everyone using the old
version should have upgraded already so I'm not sure it's necessary now.
Because Ubuntu 16.04 is an LTS, we'd have to keep the Breaks/Replaces
until 18.04 if we did add them.

-- 
You received this bug notification because you are a member of Desktop
Packages, which is subscribed to evolution-data-server in Ubuntu.
https://bugs.launchpad.net/bugs/1617693

Title:
  package evolution-data-server 3.21.90-0ubuntu2 failed to
  install/upgrade: trying to overwrite '/usr/lib/systemd/user/evolution-
  addressbook-factory.service', which is also in package evolution-data-
  server-common 3.20.2-0ubuntu1~xenial1

Status in evolution-data-server package in Ubuntu:
  Invalid

Bug description:
  upgrade to 16.10

  ProblemType: Package
  DistroRelease: Ubuntu 16.10
  Package: evolution-data-server 3.21.90-0ubuntu2
  ProcVersionSignature: Ubuntu 4.4.0-34.53-generic 4.4.15
  Uname: Linux 4.4.0-34-generic x86_64
  ApportVersion: 2.20.3-0ubuntu7
  Architecture: amd64
  Date: Sat Aug 27 22:46:34 2016
  DuplicateSignature:
   package:evolution-data-server:3.21.90-0ubuntu2
   Unpacking evolution-data-server (3.21.90-0ubuntu2) over 
(3.20.2-0ubuntu1~xenial1) ...
   dpkg: error processing archive 
/tmp/apt-dpkg-install-DNws2R/149-evolution-data-server_3.21.90-0ubuntu2_amd64.deb
 (--unpack):
    trying to overwrite 
'/usr/lib/systemd/user/evolution-addressbook-factory.service', which is also in 
package evolution-data-server-common 3.20.2-0ubuntu1~xenial1
  ErrorMessage: trying to overwrite 
'/usr/lib/systemd/user/evolution-addressbook-factory.service', which is also in 
package evolution-data-server-common 3.20.2-0ubuntu1~xenial1
  InstallationDate: Installed on 2015-10-28 (304 days ago)
  InstallationMedia: Ubuntu-Server 15.10 "Wily Werewolf" - Release amd64 
(20151021)
  RelatedPackageVersions:
   dpkg 1.18.10ubuntu1
   apt  1.3~rc2ubuntu3
  SourcePackage: evolution-data-server
  Title: package evolution-data-server 3.21.90-0ubuntu2 failed to 
install/upgrade: trying to overwrite 
'/usr/lib/systemd/user/evolution-addressbook-factory.service', which is also in 
package evolution-data-server-common 3.20.2-0ubuntu1~xenial1
  UpgradeStatus: Upgraded to yakkety on 2016-03-12 (169 days ago)

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