It appears that when fish fall through passable blocked, they hit the ground and rubber band back in weird way. Thought it was a visual glitch but it seems that they receive additional fall damage and die instantly.
I've done the test with both fence gates and signs and both seem to have the same effect. Also tested with each type of fish. (Cod, Salmon, Puffer fish, tropical fish.)
Is this still an issue for you, or did it get fixed in the meantime?