Pls how do I go about this

My company recently gave us our TAX clearance certificate covering 3yrs & it will expire in few months.

The discrepancy btw what was paid as tax for me & what has been deducted for this 3yr as tax from my salary is too much.

In such case, do you ask the company to pay you back the difference or ask for a new certificate that shows what was actually deducted?

PS
I'm aware that i could lose my job for asking management, I have always suspected that something was off cos what was being deducted was outrageous & they refused to tell us what percetage they were using

Any ideas