If my ex and I share joint legal and physical custody of my daughter and have her equal time, if she makes more money then me should I be paying support?

It all depends on several factors, including, who pays for the child's health insurance, is it really 50% physical custody, and whether the mother pays for other things such as child care.  If she pays for health insurance and child care out of her own pocket, you may have to pay her child support.  However, you should get some credit for the fact you spend significant time with your daughter.

If you believe child support services made a mistake, take the time and spend the money for an attorney's office consultation.  You may have to seek relief through the court.