There is no contradiction. An analogy of an evolving system is the automobile. Changes have been made to its various components throughout the many decades since its invention. If you take out one of the components, for example, the starter, the alternator, the engine, the tires, or the steering wheel, then it is not going to run. However, there are components that can be removed and the car still runs. For example, if one removes the rear seats, the top of the car (making it a convertible), or the trunk (making it a hatchback), the car is still functional.
Similarly, if you remove parts like the clitoris (a practice known as genital mutilation that is still practiced in some African countries) or if you circumcise a male, they can still reproduce. OTOH, if a vasectomy is performed or if the male testicles are removed, there will be infertility. So, if the genes that code for the clitoris or the foreskin are disabled, there is no impact on fertility. You cannot argue that the foreskin or clitoris are not the product of evolution, since they were not present in the beginning when sexual reproduction first evolved. In fact, the penis did not evolve until after amphibians have evolved into reptiles, but sexual reproduction evolved long before amphibians evolved. Just like the car, there are some components of the reproductive system that cannot be disabled and some that can be without causing system failure.