Thank you for playing!
I'm not sure why that bug is happening for you where you can't remove blocks, are you sure you were right clicking? Because to remove a block you have to right-click on the block you want to remove. I tested it myself and it should be working... Note, to remove blocks you also have to not be in play mode, you can press space to reset the vacuums to their original starting positions and then you can place or remove blocks.
As for the other way of solving the levels, that's actually intentional, nice job finding that way