To oversimplify, every human has an X chromosome and it is necessary to survive. The Y chromosome is optional and codes for some additional traits that make a person male. Chromosomes aren't foolproof and genes and in some cases entire chromosomes can essentially be turned off. However, since we have two of each chromosome this is often not a problem. So, if parts of the Y chromosome turn off, you potentially turn off the mechanisms that make a person male. In which case the person would remain the default of female.