I have a similar issue to another one that's been posted about a boat, but mine occurs just after I've entered Mt. Orion, and I've put the plant on the altar, the boat comes up onto the surface, I get in it, and it moves towards the entrance to the cave system, but drops me in the water. Sometimes I can move back down which brings me back to where the altar is, but then another boat appears and I can go back to the general area that I need to go, but still in the water.
Hopefully this explains it well enough. I can probably do screenshots if I need to...
Can anyone suggest anything?

When I put the pomegranate on the altar the boat came over but in the wrong place. I had to go back out of the cave and return to get the boat in the right location.