How can the existence of a living organism with both male and female characteristics be reconciled with the Almighty’s saying: "And of everything We have created pairs, that you may reflect"?

There is no contradiction between Allah's pronouncements and His actions. Allah's statement, "And We created pairs of all things that you may remember" (Quran 51:49), does not exclusively mean male and female. Rather, it encompasses diverse categories and types. Pairedness (zawjiyyah) means a category or type, as stated in the exegeses of Ibn al-Jawzi and Ibn Faris. This aligns with the Quran's use of the word for meanings other than masculinity and femininity, such as in His statement, "Do not extend your eyes toward what We have given to pairs of them for enjoyment" (Quran 20:131), meaning categories of them; and "pairs of diverse plants" (Quran 20:53), meaning different types; and "and you were three pairs" (Quran 56:7), meaning three categories. Accordingly, self-reproducing organisms fall under the meaning of pairedness as a category and type, even if they combine male and female characteristics within themselves. They are a pair because they require a partner for reproduction, with one acting as the male and the other as the female.