I reproduced it by installing a dummy 1.24 version which goes into /opt/click
After an update to ota5 /custom/click contained the latest 1.26 version but the 
system still reported 1.24 as the active version

click pkgdir com.canonical.scopes.fbphotos
/opt/click.ubuntu.com/.click/users/phablet/com.canonical.scopes.fbphotos



** Also affects: click (Ubuntu)
   Importance: Undecided
       Status: New

** Changed in: canonical-devices-system-image
   Importance: Undecided => Critical

** Changed in: canonical-devices-system-image
       Status: Incomplete => Confirmed

** Changed in: canonical-devices-system-image
    Milestone: None => ww34-2015

** Changed in: canonical-devices-system-image
     Assignee: Kyle Nitzsche (knitzsche) => Pat McGowan (pat-mcgowan)

** Changed in: click (Ubuntu)
       Status: New => Confirmed

** Changed in: click (Ubuntu)
   Importance: Undecided => Critical

** Changed in: click (Ubuntu)
     Assignee: (unassigned) => Michael Vogt (mvo)

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https://bugs.launchpad.net/bugs/1479001

Title:
  OTA update: lower user click not updated by custom tarball higher
  click

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