(A) One perplexing result of General Relativity is the prediction that gravitational singularities lie at the hearts of black holes, a point where the laws of physics no longer seem to apply, and that has been supported by subsequent research.
“a point where” is the appositive that supposedly refers to a singular noun ahead. However, there is no such singular noun in front.
(B) One perplexing result of General Relativity is the prediction at the heart of each black hole of a gravitational singularity, a point at which the laws of physics no longer seem to apply, but a prediction that has been supported by subsequent research.
“the prediction at the heart of each black hole” this part implies that the prediction exists at the heart of each black hole. Unintended meaning.
(C) One of the perplexing results of General Relativity is the prediction, supported by subsequent research, that at the heart of each black hole lies a gravitational singularity, a point at which the laws of physics no longer seem to apply.
Correct answer because now an appositive correctly refers to “gravitational singularity”
(D) The prediction of a gravitational singularity at the heart of each black hole, a perplexing result of General Relativity but one that is supported by subsequent research, is a point where the laws of physics no longer seem to apply.
this choice literally says that the prediction is a point where the laws no longer apply. Unintended meaning.
(E) The prediction that at the heart of each black hole lies a gravitational singularity, a point at which the laws of physics no longer seem to apply, is a perplexing result of General Relativity but supported by subsequent research.
In the construction “A but B” elements should be parallel. However, here A is a noun and B is an adjective.
So C