"They are not rocks."
If you were pointing at a group of Klingons and wanted to say they aren't rocks, you'd say naghmey chaHbe'.
If you were pointing at a group of chairs and wanted to say they aren't rocks, you'd say naghmey bIHbe'.
When the course gives you They are not rocks and asks you to translate into Klingon with no further context, it should allow either translation. You have no way of knowing whether the sentence-writer was thinking of beings capable of using language or something else.
This is especially true in a Star Trek context, where sometimes beings capable of using language do, in fact, resemble rocks. Remember the Hortas and Excalbians? nagh ghaHbe' Hortavetlh'e'.
We would normally expect that the subject and object should match gender (here I mean grammatical type, not sexual gender), but there are times (especially with a negative like this) where they won't match - in which case, you probably wouldn't be faulted for choosing either option. So, theoretically, yes, there might be rare instance where you could use chaHbe' in a sentence like this. Except in this course! Here we expect you to imagine a context where they match. Unless we somehow make the mismatch explicit, in which case we would probably accept either answer.
You've hit upon an area of grammar where we don't have much data: asking whether language-using nouns and non-language-using pronouns, or vice-versa, can be linked. We don't really know. To my knowledge, Marc Okrand has never used a sentence where this kind of mismatch exists.
For what it's worth, I think if you were pointing to a group of Klingons and wanted to say they're not rocks, you'd say naghmey chaHbe'. You'd use the generic, non-language-using plural suffix, because rocks don't use language. But you'd use the plural, language-using pronoun because you're using the pronoun to refer to the Klingons, not the rocks.
Dr. Okrand has made some statements about things maintaining their proper plurals even when obviously referring to something else - like the plural for the bent handles on nevDaghmey being called DeSqIvDu'. I would expect that since you are saying that they are actually animals and not speech-capable beings, you would use the proper -mey plural, or better yet leave the plural off altogether to avoid the question.