I'm trying my best, but still have absolutely no idea what that means. How is the top bolt on the stem "clamping more" than the bottom one? It's a CF steerer, you should be using a torque wrench or Torqkey. Per the Cervelo manual, the top of the steerer tube should be at least 3mm below the top of the stem, so that the top cap doesn't hit the lip of the aluminum insert.

If by "top stem bolt" you mean the bolt through the stem cap-- and that it is bottoming out, allowing the stem/fork to still rotate, then the stem is too low and needs a larger spacer underneath it.