I recently (just yesterday when it became available to me) merged my accounts, Primary being a LR3 NSW account, with a MR4 PC account that was at the [howl of the Kubrow] quest, incubating a kubrow, during which i merged. That is where the bug occurred, since I already had an active pet on my Primary account and the process got interrupted(?) on my PC account that now locked me out of using *ANY* of my pre-existing pets or even trying to finish the incubation, since I have a kubrow roaming my orbiter and i cannot access the incubator without getting kicked right back out again.
Or to sum up what may have messed things up so it may end up getting fixed (because i really would like to be able to use my smeeta or Lotus print kubrow):
When you have an incubation going and decide to merge accounts, that just breaks things, so wait with it.