It is our material thinking that is hindering us. You are thinking male, of the material world, and a male in the material world cannot produce a child. And if you think also that Krishna is mother, again you are thinking with material conception. So we have to avoid using our material thinking and material concepts when we think about Krishna. Therefore, we have to approach a bona fide spiritual master in order to understand.
Another example is explained in the Bhagavad-gita, that Krishna begets the living entities, within the womb of material nature. The material nature is also expansion of Krishna's potency. The potency is not different from the potent. Just like the heat is not different from the fire. In other words, heat and fire is the same thing; so if we talk in that way, the material nature is the mother and Krishna is the father. But material nature being non-separable from Krishna, Krishna becomes both father and mother at the same time. The heat is fire and the fire is heat. Although you can bear the intensity of heat, but if you put into the fire, you will be burned. The heat and fire are simultaneously one and different. That is the philosophy of inconceivably one and different, expounded by Lord Caitanya. Try to understand in that way.