This is a bug that might appear after the game saves your progress automatically (each time you beat a Stage). However, I don't know yet why is this happening, but if the bug appears on your system, just close and reopen the game, and load your save file from the menu. It will allow you to access the upper area of the stage. The bug appears, occasionally in Stage 3 too.
It seems to be an Engine's bug, because the code appears working perfectly in the Debug Process.