Explanation:

Correct Answer is (e).I. The problems faced in filing returns and uploading documents by those paying GST has forced the government to extend the last date for uploading yet again.
This is grammatically incorrect due to use of singular has with plural problems.  
II. The problems faced in filing returns and uploading documents by those paying GST has exposed the claims of government departments that the GST structure and GST Network (GSTN) will be ready for immediate implementation.
This is incorrect in terms of grammatical sentence structuring. The problems have been already faced, claims have been exposed and thus implementation has taken place. So use of will be ready for immediate implementation is erroneous.
III. The problems faced in filing returns and uploading documents by those paying GST has also created confusion by giving taxpayers the option to directly file their returns on the website. 
This is incorrect in terms of context. The sentence appears disjointed. How/why will taxpayers be given the option to directly file returns on website when there is are problems faced in filing returns and uploading documents on it?
Hence, option E is correct.