Hey, I am on my second playthrough of the game and found a couple broken doors when retreading old ground.
First of all, the back door out of this tree and water puzzle (which I believe goes back to the central garden) is closed, but cuts to an empty void when I walk into the doorway:
After triggering that, a short while later walking from the blue gears/water hub into the main transition gave me a similar bug where I could no longer enter the transition area because the portal would turn into a wall:
I then tried saving and reloading, but it hung while loading the save and I had to quit the game.
Restarting the game and reloading my save fixed the issues, although I have not tried going through the first door again.
By the way, these hidden puzzles and areas are rad.