You should be able to shoot the fish, they're just a bit small. With the default gun red fish take 3 hits and swordfish take 2, maybe that wasn't expressed clearly enough in the game.
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No, it's really valuable feedback. I only added an audio cue to hitting an enemy last minute, and before that it wasn't really clear that you were actually damaging them. I'll probably add a small particle effect, or see if I can alter the shade of the sprites for a few frames so there's a visual cue too. Thanks!