Not sure if this is the same problem, but I've found that if I go to my animal list and sort alphabetically by name (if known), I'll sometimes find be able to find it and move the animal from that page, even if it doesn't appear anywhere else. From that same long animal listing, I can also sometimes sort by location for quarantine, and find it that way and move them somewhere else from that screen (often having more luck moving them to the trade center than directly to a habitat). This has worked for me for some animals who show up on the long animal list, even when my quarantines all say they're empty and when they won't show up anywhere else. Or when I've got a warning/notification about the animal.
In some cases I've found that this process releases whatever hold had been on the animal and I can once again move them normally. In other cases, I've found that the animal disappears (really was a ghost, I guess), but at least I stop getting notifications and warnings about it.
Not sure what causes the animal to go into this limbo state to begin with, although in some cases I've noticed it after a crash or lost connection to the franchise server, and in one case I recognized that the animal was showing up as a quarantine ghost after I'd transferred it into another franchise zoo. So I'm guessing it is because some remnants of an animal's information is showing up in more than one place.
Good luck!