Just before its return to Earth from Mars, the “sick” robotic rover

Option E

The sentence says that just before it returned from Mars to Earth, the robotic rover got ‘sick’: i.e., it did not function correctly. It did not reveal the existence of significant organic compounds.
The phrase “significant organic compounds” is followed by “when it was present”. Logically, the sentence should state that the rover missed revealing these compounds when they were present. So, we need to infer the correct meaning here because “it” is used incorrectly. So, the meaning of the sentence is that the rover missed showing these compounds when they were present and indicated that they were there when they were not present.

As found in the meaning analysis, the singular pronoun “it” does not agree in number with the plural antecedent “compounds”. This error also leads to a subject-verb agreement error in the use of the singular verb “was”.
This choice also has the pronoun-antecedent number agreement error as in Choice A. Furthermore, the comma + verb-ing modifier “indicating” incorrectly modifies the preceding clause. As per the original sentence, this action should be parallel to the verb “missed”.
The singular modifier “that was” incorrectly refers to the plural noun “compounds”.
There is no preceding noun to which the relative pronoun modifier “which” can refer.
This is the correct answer choice. It clearly and precisely communicates the intended meaning of the sentence.