This is actually in systemd, not systemd-shim.
I patched systemd-shim to ignore unknown unit warning, so then I get a warning 
from systemd-logind: systemd-logind[1414]: Failed to start user service: 
Message did not receive a reply (timeout by message bus)
So it's being started by the login manager once pam-systemd registers the 
session.

pam_systemd manpage: A new systemd scope unit is created for the session. If 
this is the first concurrent session of the user, an implicit slice below 
user.slice is automatically created and the scope placed
           into it. An instance of the system service user@.service, which runs 
the systemd user manager instance, is started.

I'm guessing user@.service is generated at runtime by systemd (which
would require systemd is init, not upstart).

Suggestions for fixing this:
1. Move /etc/pam.d/systemd-user to the systemd-sysv package (assuming none of 
systemd-logind's features are required)
2. Patch systemd-logind to not start the user service if the system wasn't 
booted with systemd

I'll take a look at patching systemd-logind.

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https://bugs.launchpad.net/bugs/1359439

Title:
  [    7.287663] systemd-logind[1057]: Failed to start unit
  user@126.service: Unknown unit: user@126.service

Status in systemd-shim package in Ubuntu:
  Triaged
Status in systemd-shim package in Debian:
  New

Bug description:
  ATTENTION: This bug is fully understood, there is *no need* to add
  even more comments about "me too" here.

  [    7.287663] systemd-logind[1057]: Failed to start unit user@126.service: 
Unknown unit: user@126.service
  [    7.287677] systemd-logind[1057]: Failed to start user service: Unknown 
unit: user@126.service
  [    7.293871] systemd-logind[1057]: New session c1 of user lightdm.
  [    7.293902] systemd-logind[1057]: Linked /tmp/.X11-unix/X0 to 
/run/user/126/X11-display.
  [    7.363706] ip_tables: (C) 2000-2006 Netfilter Core Team
  [    7.421846] nf_conntrack version 0.5.0 (16384 buckets, 65536 max)
  [    7.484529] IPv6: ADDRCONF(NETDEV_UP): virbr0: link is not ready
  [    9.903052] wlan0: authenticate with c8:d7:19:22:21:ec
  [    9.912429] wlan0: send auth to c8:d7:19:22:21:ec (try 1/3)
  [    9.920181] wlan0: authenticated
  [    9.924352] wlan0: associate with c8:d7:19:22:21:ec (try 1/3)
  [    9.925709] wlan0: RX AssocResp from c8:d7:19:22:21:ec (capab=0x11 
status=0 aid=2)
  [    9.927753] wlan0: associated
  [    9.927800] IPv6: ADDRCONF(NETDEV_CHANGE): wlan0: link becomes ready
  [   12.677104] systemd-logind[1057]: Failed to abandon scope session-c1.scope
  [   12.677122] systemd-logind[1057]: Failed to abandon session scope: No such 
interface 'org.freedesktop.systemd1.Scope' on object at path 
/org/freedesktop/systemd1/unit/session_2dc1_2escope
  [   12.683902] systemd-logind[1057]: Failed to start unit user@1000.service: 
Unknown unit: user@1000.service
  [   12.683912] systemd-logind[1057]: Failed to start user service: Unknown 
unit: user@1000.service
  [   12.685157] systemd-logind[1057]: New session c2 of user caravena.
  [   12.685190] systemd-logind[1057]: Linked /tmp/.X11-unix/X0 to 
/run/user/1000/X11-display.
  [  234.494462] systemd-logind[1057]: Failed to abandon scope session-c2.scope
  [  234.494478] systemd-logind[1057]: Failed to abandon session scope: No such 
interface 'org.freedesktop.systemd1.Scope' on object at path 
/org/freedesktop/systemd1/unit/session_2dc2_2escope
  [  235.514349] systemd-logind[1057]: New session c3 of user lightdm.
  [  244.245908] systemd-logind[1057]: Failed to abandon scope session-c3.scope
  [  244.245923] systemd-logind[1057]: Failed to abandon session scope: No such 
interface 'org.freedesktop.systemd1.Scope' on object at path 
/org/freedesktop/systemd1/unit/session_2dc3_2escope

  ProblemType: Bug
  DistroRelease: Ubuntu 14.10
  Package: systemd 208-7ubuntu4 [modified: 
usr/share/dbus-1/system-services/org.freedesktop.systemd1.service]
  ProcVersionSignature: Ubuntu 3.16.0-9.14-generic 3.16.1
  Uname: Linux 3.16.0-9-generic x86_64
  ApportVersion: 2.14.6-0ubuntu2
  Architecture: amd64
  CurrentDesktop: LXDE
  Date: Wed Aug 20 18:26:06 2014
  InstallationDate: Installed on 2014-04-27 (115 days ago)
  InstallationMedia: Ubuntu-GNOME 14.04 LTS "Trusty Tahr" - Release amd64 
(20140416.2)
  SourcePackage: systemd
  UpgradeStatus: No upgrade log present (probably fresh install)

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