I've run into the same error a couple of times now.
My first play through the game I got to where I had completed the purple level, but when putting in the purple world-building cube the purple tree is created but the world isn't created. I can't progress further from that point without the purple world being built.
Additionally, I can't save the game at that point. The last saved game from that play through is from near the end of the purple level when I am falling to get the dark cube. I can't save anything after that.
I have tried running through the game again, but have hit the same issue with the red level. My saves aren't working.
It seems like this is a somewhat common issue in these forums. I would like to complete the game, particularly from my first play through, but there is a significant bug preventing that.