For some species I'd say it's less a question of where they are kept but rather a question where the heck they are actually breeding them. Take matamata (not yet considered endangered I know) and fly river turtle for example. Both are pretty common around the world, but in Europe there is only one breeding record of matamata in zoos and only 3 zoos that either are or have bred fly river turtles. In a US private care manual I also read that the writer knew of only one single breeder of matamata in the US private sector. And yet both species are on the regular kept in non-breeding setups and/or in mixed exhibits with aggressive fish, crocodilians and even snakes. Some other species where this happens on the regular are Chinese soft-shelled turtle and snapping turtles. Many holders, many single specimens and as far as I know no breeding at all in European zoos (except for the Central-American snapping turtle). For these species we do have the luck that there are farm-bred specimens available, but that's not the case for every species.
I'd say especially for the bigger species this is a big problem. In Pairi Daiza I've seen several rare and endangered turtles and tortoises (some rare in zoos, some rare in the wild, some rare in both) and the amount of single individuals, non-breeding groups, bad social groups and/or horrendous mixed exhibits is astonishing. This included species like matamata, brown tortoise, Ploughshare tortoise and Chinese soft-shelled turtle.
To end on a positive note. My local zoo keeps some rare species like Elseya branderhorsti (VU, handfull of zoos, first breeding in European zoos a.f.i.k.), Cuora amboinensis (EN, couple dozen zoos, bred from time to time) and Pelusios sp. (LC, two species kept in no other European zoo, first breeding two years back). They also keep an Nile soft-shelled turtle, but it's kept alone in a fish-tank sadly enough. Their Nubian flapshelled turtle was also kept alone with the Pelusios sp. so it never bred.