When a normally functioning immune system attacks a non self molecule,

In the text as well as in A, the pronoun 'it' refers to the system without any doubt. There may be naïve attempts to justify that 'it' may antecede either the system or the non-self molecule or the foreign body or the species or any other singular noun available in the passage. But nope; The first right of the pronoun is to refer to the subject, failing which it may seek other nouns. We have a handsome subject in the form of 'system' and in such a copybook situation, why would the pronoun seek any other noun.

However, D defensively substitutes the pronoun and says that the immune system reacts accordingly. It leaves no doubt whatever. Both A and E are correct.

I would personally fancy A to D, even though I suspect that the OA may prefer D.

I don't think there is any logic in B, C, and E.

IMO the correct answer is D

When a normally functioning immune system attacks a non self molecule, the system has the ability to "remember" the specifics of the foreign body, and upon subsequent encounters with the same species of molecules, it reacts accordingly.

A. it reacts - Pronoun ambiguity, "it" can refer back to any singular nouns presented earlier in the sentence. - INCORRECT
B. the foreign body reacts - Meaning issue - INCORRECT
C. the molecules react - Meaning issue - INCORRECT
D. the immune system reacts - Removes the pronoun issue & re-applied the noun to make proper sense - CORRECT
E. the species react - Meaning issue - INCORRECT

Official Explanation

Correct Answer: D

Choice a is an unclear sentence because it could refer to several antecedents, including foreign body, molecules, immune system, and species. The correct antecedent is immune system. Choice e also has an error in subject-verb agreement (species requires a singular verb reacts).