Imma test and get back to you. I thought I covered that edge case but I'll walk back through and confirm.
Holy ?! It is a bug! I will patch this in a future release, but for now you can type ?noclip to get yourself back in the skypertube and type ?clip once you're inside to finish the puzzle. Thank you for finding this, I have in my notes that I tested this exact scenario, so it must have regressed at some point.