With the exception of from transports (thus I always figured it was an unlisted ability of them or for a later tech), I had never been able to (nor had the AI) attack from sea before without amphibious assault.
And yes, that's exactly what happened.... the first time I tried the official patch, right from the get go, I had barbarian swordsmen attacking my swordsmen on my galley that was at sea. I hadn't saved it before then (I don't usually save until well after that point), and I just quit the game after my "What a load of crap!" exclamation after losing my units that should have been safe at sea (again, at least from land units).
Well, I just tried a small testbed, and I couldn't attack an enemy's units on a ship, from land.
I'll need to see you either post a game file or a test bed, to check if what you are saying is true. Until then, I'm assuming the game does not allow land-to-ship attacks, which is always the way it's been in every game I've played. (Including the 3.17 patch.)
I'm not using Solver's patch, so perhaps that is the difference. (If Solver broke something.) But you seem to be claiming that it's not a bug with Solver's unofficial patch.
I suspect you didn't properly take note of the combat. Maybe there was a fort involved or something like that.