Other mistake: Technically, this movie should be called, "I Still Know What You Did The Summer Before Last Summer" since the events take place the summer after the end of the first movie. That would be two summers after the events of the beginning of the first movie. (00:01:05)
Other mistake: Titus emerges from the pool, scaring Karla and Ty, and he has weed which he immediately smokes despite it previously being underwater and unlit. (00:44:25)
Other mistake: When Karla and Ty are in the jacuzzi, the "Bob Marley" guy shows up and says they can't be there because it's after midnight. At the same time, the fisherman is killing the hotel's maid who is knocking on doors to clean the rooms. Why in the world does the cleaning lady do the housekeeping after midnight?
Other mistake: Toward the end of the movie a helicopter with a US Coast Guard paint job shows up. The island is in the Bahamas, which has their own Coast Guard, it is highly unlikely the USCG would be the ones responding to the island.
Answer: I think that Estes already knew that Will was Ben's son. He had made a comment about a man (Ben) killing his wife (Sarah) in the same room Julie and Will was staying in. He also makes a comment about Will having his mother's eyes. So he probably recognized him. He also knew that the answer they gave to the radio host was wrong, and that proved it was a set up from the beginning.