How to reproduce:
1) Use color gun to paint buildings blue (that was the resulting color from flower petals for me, didn't see a way to switch color). Paint the HUB, Space Elevator, Miner, Power Pole etc.
2) Save the game.
3) Load the game using the save from 2) or Continue after closing the game.
4) Check color on the buildings mentioned under 1). All of them are still blue with exception of the HUB, which is orange again.