Many of the phase out species were/are on their way out anyway - when a species can't be kept going without relying on imports, that isn't worth it. Sun Bear is a good example of this. Despite trying for years success in breeding them was near zero and they are aging out. Space is the other prime issue, and when there's too many contenders for a specific slot, someone has to get cut. This has been the case for Gaur, which has a smaller population than Banteng.
They're not being 'malicious' about it at all, the AZA is trying to keep stable, genetically viable populations going for the long term. If the founder population is small or poor genetically, they're almost always going to be first on the phase-out block. Especially true for hoofstock, because once we lose a species, regulations are such we're not likely to ever get them back. Even when a species is numerous genetics can still get in the way - Masai Giraffe is having increasing issues with inbreeding depression due to a small founder base. A species can be rare and in need on conservation help, but if your founder population is tiny or struggling, it's not always going to work out.