Subject/Verb agreement? Thanks!

       
It
was anomalies in the orbit of Uranus that led to
the discovery of Neptune.

            

            A) It was anomalies in the orbit of Uranus that

            E) The anomalies in the orbit of Uranus was
what

            

            My pick was E), because it looks more concise to me.
However, the correct answer is A). The explanation is that the subject and verb
don't agree in E). Doesn't the same error apply to A) given the explanation on
E)?

Any suggestions
will be greatly appreciated!