Revealing mistake: When Truman is first discovered escaping on the boat, they go to a camera shot of his face. If you look at the water, the boat is not moving at all. They use a similar shot later in the scene after the storm. You can also tell the background is the same as the large wall that Truman crashes his boat into. (01:19:05 - 01:25:25)
Revealing mistake: If you look in Truman's car's mirror when he is backing up from the traffic jam, wires can be seen wrapped around his car.
Answer: He'd been hoping the waves would discourage Truman and make him turn back. It's a lot easier to agitate water than it is to calm it, so by the time he saw it wasn't working, even if he's thought of that, it would have been too late.
Captain Defenestrator