Having worked in one of the largest wholesale suppliers for freshwater ornamental fish in the US, I've bagged a fish from almost every genus in the hobby. Here are the "hardest" species, both in terms if catching the fish and doing it without injuring them:
-Freshwater shrimp are absolute NINJAS. #1 on the list!
-Otocinclus catfish
-Pictus catfish
-Pea puffers
-Hillstream loaches
-Spiny eels
-Sting rays
-Catching any tiny schooling fish in LARGE numbers and accurately counting them. Example: catch 100 cardinal tetras in a tank of 160, count them accurately, and you cannot handle them roughly or they will NOT survive shipping.
Many people don't know how to catch fish efficiently IME. You DO NOT chase them with a net--you chase them into the net with your other hand if you can. You have to learn how fish swim and react to a net. It took me a couple months of doing it 40 hours a week to get good at it.