Oh no! Sorry to hear you got stuck. :( I didn't have much time left to betatest it, but it is definitely possible to complete the game.
A tip to avoid this bug: Once you have access to a new map just stick to that map (so no backtracking to a previous map).
Viewing post in Captain Silver's Secret Treasure jam comments
No worries! It was a breeze to get there, and the random event rolls lends itself to more playthroughs, anyway. I posted a "please don't do this so as to avoid bugs!" section on my jam page, so I totally get how it is. :D
Not sure if this'll help you isolate the issue I ran into, but my route went like this (and was backtracking-free!): On map #1, I went to the southernmost area, then the three top ones from right to left; on map #2, I went up, then down, and then left, where the cutscene/boat-napping happened.