i dare say we need some corrections with underlined part of the sentence, as far as i read
my vote for A

Gmatmachoman - what happen to you man. Not concentrating on the forum???? you are getting distracted huh anyways, I have corrected the underline part

IMO ans is A

Fossils of a whale that beached on an African shore more than a million years ago and
was subsequently butchered by hominids have been recovered by paleontologists.


A. that beached on an African shore more than a million years ago and was
subsequently butchered by hominids have

B. that beached on an African shore more than a million years ago and then was
subsequently butchered by hominids has

C. that beached on an African shore more than a million years ago, which was
subsequently butchered by hominids, has

D. having been beached on an African shore more than a million years ago and
subsequently butchered by hominids, have

E. having beached on an African shore more than a million years ago and then
subsequently were butchered by hominids have

Great GMAT question, the crux to crack such question, an in GMAt questions, lies in identifying the subject of the sentence.
1. Subject is Fossils, which is plural
2. the clause starting that beached....., is describing whales and not fossils

First to eliminate B\C as those are simplest.

B & C has 'has' refering to fossils hence INCORRECT.

D has below error:

D. having been beached on an African shore more than a million years ago and subsequently butchered by hominids, have

that leaves out with A & E:

If clause starting that describes fossils then E is logically correct because of plural were in that clause(highlighted below_

However I feel that is not the case and its describing whale and hence should be A.

E. having beached on an African shore more than a million years ago and then subsequently were butchered by hominids have

Hence answer should be A.

Hope that helps!