The reason that calico cats are almost always female is due to the inactivation of the X chromosome in different cells. All females have two copies of the X chromosome, one inherited from each parent. During fetal development, there is a period when the cells are dividing and both X chromosomes are active. However, after a certain point, one of the two X chromosomes gets inactivated. But this happens randomly, so by the time you have a fully developed animal, you have scattered populations with copies derived from one of the two X chromosomes. The coloring in the fur is controlled at least in part by genes on the X chromosome, so you have patches of fur of different color, each the result of its active X chromosome.

The inactivated X chromosome can be seen in a cell under the microscope, and is called a Barr body, after the biologist who first described it.