I figured the prince was still in Dorne in mourning. Forgot he was on the boat.

It's easy enough to figure out some of the answers to the questions you're asking-- two Sand Snakes follow in a small, quick boat to kill the Prince, Jamie didn't feel compelled to kill the Prince on what I imagine was a Dornish boat with a Dornish crew, and he's also probably savvy enough to realize that if they killed homegirl right in front of him that they'd be waiting to kill him as well...

... but it's also easy enough to include those explanations quickly. One quick shot of a small boat following the boat with Jamie and them. A shot of Jamie looking angrily at the Dornish crew around him, or saying "I can't sail this boat after killing every Dornish man on it" or something like that. The Prince saying to the Snakes, "Why did you two follow me here?" to establish the relative position on the map better. Those things could've taken, what, thirty seconds in an episode that's under fifty minutes long?

I usually have no long-term beef with the off-screen plot points they skip, because I usually get that they have bigger long-term narrative fish to fry, and while that was almost certainly why they did what they did here, these questions (and a few others, I'm sure) are such easy fixes that it is somewhat disappointing that they'd leave us confused like this.