Transphobia isn't always intentional, but it's a pain -- story I heard yesterday.
Lee is a trans man. He and his husband decided to have a baby, as Lee's uterus and ovaries were functioning. At the hospital, the delivery-monitoring systems were unable to work, because legally (and therefore medically) Lee was male and therefore anything to do with obstetrics was right out.
Now why would you design software so that a detail of the patient's lagal ID rules out a whole class of functions?