Ya I've noticed this for a while now. It also does this for equipment cooldowns. It's easily replicated on hedo. Do a phase 1 and you should still have over half of your kraken armor on CD. Swap to another app for a few seconds then swap back. You'll notice the armor proc hasn't moved, but will finish its cool down before the Hud icon actually reaches the zero point. It kind of disappears.
Was interested though and just tested it seems the pet cooldown stops counting when you swap apps and only starts when you come back. Example hero pere CD of 15secs will be 18secs if you are swapping apps for 3 secs.
Not sure why one cooldown would continually countdown and others wouldn't.