Check out for the redundant, verb tense, and the subject-verb agreement.
The subject into consideration here is Fossils which is PLURAL, and the complement verb HAVE should be used in this regard to satisfy S-V agreement. Note: the statement being referred to here happened a million years ago, and this is an indication that it occurred in the PAST, and as such, past tense "WAS" must be used to validate the singular noun "a Whale" in this question.

Option A - Correct
The sentence has a passive tone and requires simple past. Thus, this option further satisfies the S-V agreement (on Plural subject "FOSSILS" being used with a plural verb "HAVE") and incorporate the correct past tense format.

Option B - Incorrect
A plural verb "HAVE" should be used in this context instead of "HAS" which doesn't satisfy the S-V agreement.

Option C - Incorrect
Which is a misplaced modifier. Also, "HAS" needs to be in its plural form.

Option D - Incorrect
The passive phrase "having been beached" is not required because "Whale" received the actions; therefore, cannot split a subject and a verb with a comma "have"

Option E - Incorrect
..."then subsequently" is a redundant; "were" must be singular form because the noun of the relative pronoun is singular "a Whale"

Thanks.