Agree with A here
B) "the reason... is because" is redundant. It should be "the reason... is that"
C) second part or relative clause introduced by "where" has no verb:
where low-level leaks are chronic
the routine discharge of mud and mineral salts--> no verb here
D) indeed "due to the fact of" is not idiomatic
E) "along with the routine discharge of drilling mud and mineral salts" is a parenthetical element set off by commas. It can be removed and following verb should be singular.