It was X that led to the discovery of Y and A perfectly fits into this structure
1)It was the anomalies in the orbit of Uranus that
2)It was the orbit of Uranus showing anomalies that - meaning issue
3)They were anomalies in the orbit of Uranus that
4)The orbit of Uranus being anomalous was what - sounds awkward
5)The anomalies in the orbit of Uranus was what - sounds awkward

Last option has an obvious subject verb disagreement (anomalies is plural, and so, the verb should be were), but this does not look like an official question.

prernamalhotra wrote:It was the anomalies in the orbit of Uranus that led to the discovery of Neptune:

1)It was the anomalies in the orbit of Uranus that
2)It was the orbit of Uranus showing anomalies that
3)They were anomalies in the orbit of Uranus that
4)The orbit of Uranus being anomalous was what
5)The anomalies in the orbit of Uranus was what

why is option 5 wrong

[spoiler]OA :A[/spoiler]

Thank you,
Prerna

option 2- the intended meaning is wrong
Option 3 - They is used to refer people
Option 4 - very awkward
Option 5 - anomalies - were (but the option says was) so wrong.
Option 1 - It should be 'it were the anomalies' because anomalies is plural subject. But as this given in the question I go with this option.

But IMO i think there is a flaw in the question. Can you tell me what is the source?