Raw Salmon and Pufferfish caught after the 0.16.0 update do not stack with the ones caught before. Cooked salmon still stacks in all variations of catching and cooking.
Raw fish seems to stack, but I didn't pay a lot of attention to it, so I'm not sure. I didn't catch any clownfish during the time I needed to fish, so I don't know about that one.
Confirmed to affect 1.0.0 as well, new fish do not stack with older kinds, as described.