Your wife not paying into Social Security (doe to city worker) has no impact at all on your income tax on your return.
The only way you could really see what the differences are between your return and your wife's sister is to print both returns and look at them line by line to see what is different.
My guess would be taxes withheld is different, or they may have larger amounts going into retirement plans at their jobs, but only way is to look at both returns.
