It has been argued that the phrase had its origin in dice games, since dice have been called bones since the fourteenth century at the latest, for the good reason that they were originally carved from bone. The image presumably is that the player doesnt stop to call on Dame Fortune or talk to the dice after the manner of craps players (Baby needs new shoes!) but just rolls them.
A more probable, but somewhat surprising, origin is from the meal table. The oldest version of the expression is to find bones in something, meaning to find a difficulty or objection in some course of action. The first example is from one of the Paston letters of 1459. It seems to have been linked especially with soup: to have a bone in that certainly presented difficulties in eating it. To find no bones in something meant that you had no problems or difficulties. The idiom seems to have grown out of that.