This is the second day I've hit the same glitch and so have several people around me.

We get on the boat when it docks, then wait for the boat to leave (and the cutscene to start and then we zone into the boat) ...but it never happens. Oh the 'boat' is still around us, but we never get the CS, never zone. We can walk back onto land or back out to the 'boat', but we're still in Selbina and the boat has most certainty left.

The only way I managed to get ever onto the boat properly was to zone out to the Dunes, come back through (and pay MORE money ) and tried to get on the boat again. Despite doing nothing differently, that worked properly the second time. This has worked twice now to "resolve" the issue but it's not really resolving the initial problem, obviously.

I'm not sure what's going on but if someone could please look into this weird glitch, I'd be grateful!

I've been tracking on this myself. It seems that if you try to board one voyage of the selbina>mhuara ferry you can't actually physically walk onto the boat. On the next voyage you can get on to the boat but it takes off without you. I've found that if you stay on the boat at this point then the next ferry actually takes you out on its voyage. This is, I assume, the one you can't get on if you try it from outside the boat.
Also, the mhuara>selbina ferry appears to take twice as long as it should. The NPC onboard that tells you the voyage time actually starts over half way through.
Just speculation, but I think pirates may be bugged as well. I've done many voyages since these bugs started trying to get a sand charm (I wasn't counting, probably more that 20) and I haven't seen them yet. This is just a guess though. Maybe I just have bad luck.

Okay so this sounds crazy, but I think I found a work-around for this problem.

I realized every time the boat failed to leave with me, I was just standing there in the hold facing the direction I walked on (the two opposite doors that lead you to the top deck). I started turning to watch the doorway you come in through, because that was the only indicator from within the boat that the boat had left without you, and ever since then, the boat has left with me on board! I don't know why that makes a difference, but ever since I started watching the doorway (the one you come into the hold through), I have never had this glitch happen again.

Nice idea, but I think it actually works now because the bug was fixed.

This happened to me today. I was standing on the entrance ramp, fishing. In the middle of the cast, the boat began to move, but my character didn't move with it. I was then stuck on the phantom boat until the next boat arrived.