I haven't looked at the actual decision yet but I believe that the reason for overturning Bush was form of the order, namely, executive vs judicial.

I think the court held that the proper course was for the Department of Justice to seek a court order to overturn the execution/conviction. Instead, Bush issued an executive order.

Generally, executive orders are used for matters involving the conduct of the executive branch of the federal government, not the conduct of the judicial branch of a state.

Furthermore, it would seem to me that Bush could have issued a presidential pardon, which he is empowered to do, or even perhaps an order of clemency, instead of an executive order.