It is true that when God created man and then woman he said it was "very good." God blessed them and told them to procreate. But since sin entered into the world, humanity has been suffering the consequences, including sickness, disease and, ultimately, death. All sorts of things have started to go wrong with our DNA and serious problems arise as a direct consequence.
What constitutes being male or female – is it simply genetics, biology and organs? Or is there more to gender than simply the reproductive organs we're born with? What medical and scientific explanations are there for babies who are born with both male and female sexual organs (or characteristics of both organs)? And is it necessary to conduct chromosome analysis in order to establish the true sex of a baby, regardless of visual evidence of sex?
The dictionary definition of Hermaphrodite is a "Human being or animal combining characteristics of both sexes; animal having normally both male and female sexual organs, e.g. earthworm; plant in which same flower has stamens and pistils."
With earthworms, this is designed by the Creator as a normal function, also with plants. With humans it is a dysfunction - a bad case of DNA gone wrong. This very rarely occurs, but in the vast majority that do, the sex organs are undeveloped and cannot function properly. It is not normal.
Male babies obtain their Y chromosome from the biological father. That is what determines a male child, as opposed to a female child. Any child born with one Y chromosome is a male child, no matter what physical problems there might be, or how that child grows up to think about itself. Several things can contribute towards confusion as to how a child feels about its sexuality. Pregnant women can be ingesting phthalates, which are also in certain plastics (e.g. in babies bottles) and these promote feminising hormones in children. Little girls are not adversely affected by phthalates in regard to their nature, but little boys can begin to display more feminine qualities. Also, we have massive media presentation of 'gender issues' and the doctrine that homosexuality, lesbianism and all sorts of sexual practices are perfectly normal - desirable, even. This has a huge impact on how teenagers develop with regard to how they view sexuality in general, and their own sexuality in particular. It is a recipe for confusion. Chromosome analysis will determine the true sex of a baby, regardless of visual or emotional leanings.
Finally, on a spiritual note, the fact that Jesus, the Word of God, was male does not entitle us to draw any conclusions as to gender in God. Sexuality is biological, applicable to a nephesh (a living soul or an animated body) but utterly alien to one who is pure spirit. Jesus pointed out that, in the resurrection, there is no marriage union because the resurrected people are as the angels in heaven. Human sexuality is unique. It is a biological gift that develops after the foetus reaches a certain point of development, because, initially, the foetus is neither male nor female, but if the Y chromosome is present, that baby will be a male child.
The difficulty lies, not in God's creation, but in the effects of sin upon humanity. The whole of creation is groaning under the weight of sin, and only God's eternal plan of salvation will restore us to 'ease' - which is the opposite of 'disease'.