Thanks for the detailed report, it's very helpful! :)
For problem 1, I've seen people having trouble jumping out of the water. The character would sometimes 'stick' and you would have to press jump again to leave the surface. But I've never seen someone ending up outright stuck. I need to investigate this further...
For problem 2, couldn't you use the ladders to get up to the main hub?
Again, thank you for your feedback :)