Is it? It really looks like it is.
I'm not quite sure why you think it's 'winking', but this picture isn't winking :
I just checked on my X game too and the Magikarp definitely has two open eyes.
I'm sure it's not winking. As you walk around it, it's probably just the camera angle glitching up a bit. Maybe the pixels and tiny details are flickering as you walk by? But unless if it's just a little Easter egg, which it probably isn't, it's just a little camera glitch.