I ran into a small bug in phase 3, where I used a seed launcher to plant a tree under a conveyance port. The port was being counted as a building that needed to be removed, but acted like a tree in all other respects. When I exited to the main menu, and continued my game, the port was gone, replaced by the tree.
I'm enjoying the game so far though. The theme is refreshing to see, and the pixel art is lovely. I particularly appreciate the zen mode option. I look forward to playing more!