Thanks for playing and for writing this up. The fish losing interest is on purpose: a shoal held under one light too long grows used to it and sinks away, and a flare makes a risen shoal leap before it tires. The game only says so in a short message, so it is fair that it felt like a bug.
The double click on a boat firing a flare while you nudge it is a real control problem. That goes on the fix list with the early upgrade prices and the number keys.