Deductions & credits

still is not making sense to me tax return is 8700.00 then i add in his taxable pension that is 46k we paid 2k in federal outta monthly checks, then they take the whole 8700.00 plus the 2 k we already paid plus we would owe 680.00? how is that possiable that means we are paying over 10k in taxes on a 46k pension and 15k of it was a pension loan, so we only received 31k of that