When the game tells you your caught fish's location, it may be little off.
It only remembers where you were when you caught a fish, not the spot where fish bites your bait/lure! I always thought they did in this way, but I'm wrong.
It can get problematic if you're fishing in the place where two or more areas meet. If you park in Lilypad Pier and you cast far into Red Windmill, the game will think you caught a fish in Lilypad Pier, not Red Windmill. When you're catching particularly rare fish, be sure you have correct location for that fish.