I tried to reproduce it but I can't. This is what I did:
Do the tutorial after that I click on the starting nodes and started upgrading it multiple times without a cost. (I learned that when you start as long as you do not click the x1, x10, or MAX buttons above upgrade that it cost nothing to upgrade all you want) Then I bought a new node of grass and rock because the exploit I found but it still would not let me delete that 2 starting nodes, so then I upgraded the ones I bought then deleted them and then it let me get rid if the starting 2.