The objection is serious only if "pairs" is taken to mean that every organism must consist of two separate biological sexes. The Quran does not require that narrow meaning: its language can refer to complementary kinds, counterparts, and categories, while the surrounding verses explicitly include realities unknown to human beings.
Why the objection seems forceful
A critic may argue as follows: Quran 51:49 says, "of all things We created pairs," and Quran 36:36 says that God created all kinds of pairs. Yet bacteria commonly reproduce by division, many fungi do not have male and female sexes in the ordinary sense, and some animals reproduce asexually or are hermaphroditic. If the verses claim that every living thing has a male counterpart and a female counterpart, then the claim appears biologically false.
That is a fair description of the challenge. It would be weak to answer by pretending that every organism has two separate sexes. Biology plainly contains different reproductive systems, and the Quran should not be defended by changing the facts.
What "pairs" means in the Quran
And of everything We created pairs, so that you may remember.
Quran 51:49
The Arabic word azwaj means pairs, counterparts, kinds, or categories. It can refer to male and female, but it is not restricted to that meaning. Classical Quran commentators commonly explained these verses through several forms of pairing: male and female, differing kinds, opposites, and mutually related counterparts. The Quran itself gives a broad context:
Glory be to the One Who created all the pairs - from what the earth produces, and from themselves, and from what they do not know.
Quran 36:36
This verse mentions plants, human beings, and then "what they do not know." Its point is to direct people to the ordered, varied structure of creation, not to provide a modern taxonomy of reproductive mechanisms. Even within ordinary speech, "pairs" need not mean two sexes. We speak of paired categories, contrasting properties, and things that exist in relation to one another.
What the verses do and do not establish
These verses do establish that creation is not random or self-explanatory, and that God created its diverse forms, relationships, and distinctions. Sexual pairing is one clear example, especially in plants and animals, but it is not the only possible application of the word.
They do not establish that every individual organism has a male and a female body, or that every species reproduces through two sexual partners. Therefore, bacteria and asexual organisms do not refute the Quran unless one first imposes a narrower meaning on azwaj than the Arabic and classical interpretation require.
If someone insists that "pairs" must mean two separate reproductive sexes in every organism, that reading faces genuine counterexamples. But that is a disputed interpretation, not what the verses plainly say. The biological objection therefore does not demonstrate an error in the Quran; at most, it challenges an overly narrow explanation of its language.