I used to visit the Jihlava zoo pretty often, since I went to school at the town, but it actually took me a few years to spot the Siberian flying squirrels. But I was so happy to finally see them - I was just randomly passing by their cage in the late afternoon...!
Also, I saw the lowland paca only once. It usually can be seen only when it's feeding time, which is at 9:30 AM or so, and that's when I'm usually watching the bush dogs, since they're one of my favorites in Jihlava and they aren't as much active at the rest of the day...
People say it is very tricky to see the blue duikers there, but I don't really understand it...? I think people are kind of overreacting and just don't have the right timing or enough patience. They're very shy animals that like to hide, but I don't think they're that hard to spot, especially in winter, when there are no leaves on the trees.
When it comes to Prague zoo - I've never spotted the binturong in the Indonesian pavillion! Not even once! And I know I'm not the only one, which is the only thing keeping me calm - 'cause I love binturongs and I think their enclosure is actually pretty nice!
Speaking of Prague, I don't think I've ever seen the capybaras there and if so, it was only once, shortly after they arrived. Not like I mind it though.
And I've never actually seen Prague's boat-billed heron... Which makes me sad, because I haven't seen it in Zlín either.
Of course I've never seen Zlín's aardwolves...
And one last thing - I think it is pretty hard to spot the little owl in most czech zoos. Or maybe I'm just unlucky.