Sentence Correction

See attached question from GMATPrep.

I am going through each of the answer choices trying to highlight what is wrong or right (for the correct choice) with the answer choices:

(A) Issue with original sentence:
• Idiom: “associated both” (incorrect) Vs “associated with” (correct)
• Distorts meaning of original sentence: “bear traits associated both with Homo erectus and, in addition, Homo sapiens has been found in the …”
• “has been found” – what has been found ? this looks as if it is referring to Homo Sapiens … in which case it should be “have been found”.

(B)
• Idiom: associated with should be used
• “have been found” – whats been found ? the skull. So this should be “has been found”.

(C)
• Correct use of idiom “associated with”
• “has been found” correctly refers to the “million year old skull”.

(D)
this sounds wrong to my ear ... but what grammatical rule is being broken here ?

(E)
• “have been found” should be “has been found”
dont understand what is wrong with "which indicates" ... why is "indicating" better than "which indicates" ? Is this a parallelism issue ---> bearing, indicating ?

Thanks for your input.
II