Sean mimics his father. In Jaws The Revenge, Sean has become the chief of the Amity Police. He's still mimicking Martin.
The whale's eerie howls in the night? It's warning its podmates that there's a dangerous predator in the area.
Why did the shark attack and eat Alex, when there were plenty of other easily available humans? Because Alex, on his float with his arms and legs sticking out, probably looked from below like a seal or a turtle. This is one of the major causes of shark attacks in real life, where sharks attack surfers when they mistake them for their natural prey.
When Pippet the dog does not come back before the shark kills Alex. It is highly likely that the dog was eaten be the shark.
There's no "highly likely" - that's exactly what's happened. That's the whole point of showing that shot of the dog's stick just floating there. It's weird that some people consider that to be ambiguous.
When the shark charges towards Brody in the final encounter, scraps of flesh are shown around its teeth. This may have been the last we have seen of poor Quint.
In the beginning of the film, Michael Brody casually goes swimming with a fresh cut in shark infested waters. Obviously, nothing happens to him, but in hindsight...
The scene where Hooper dives into the water seems not-so-scary until the reveal of Ben Gardner's head, since he knew that the shark was not in the area due to his boat's radar. Until you realize that Brody doesn't know how to operate any of the gear and couldn't warn him if the shark did start to return.