Hm, no, it must be a bug. But I must say I experienced it few times, but I wasn't sure if really clicked in the right place. Your experience prooves it is something I should look into.
It might be cause by the fact game checks if fish is on the spot where when the boat arrives, not when you click. When you add that fish move around slightly, it might be possible that when the boat arrives, fish moved few pixel away and "fish check" on that square returns false now.
I have just checked it by playing few times and it seems to be the reason. I will fix that soon. Thanks for pointing this out!