Remember, the plan was for there to be only 6 animorphs by the Ellimist. I think those were the rules. I therefore propose two theories. Crayak and the Ellimist allowed for the cube to remain, Crayak so as to bring about David, and the Ellimist as to bring about the auxies. Or.........
The Ellimist and Crayak were not involved, it was just a coincidence and they just screwed up the first time and lucked out the second time since they are only human. Of course, it makes sense that the Ellimist was involved because control of the morphing cube was the most important part of winning the war.