When you tell your employer that you are married filing jointly you are telling them that you have an extra person as a deduction on your tax return so you won't owe as much tax for the year. Since you won't owe as much tax for the year they take less out of your paycheck.
In your case, because you both work, you don't have an extra person. That person is also earning money which - when added to yours - moves you into a higher tax bracket.
You should both be withholding as 'single'. Especially if you are married with no children. Single takes the most money out of your paycheck and if both of you are withholding that way should cover the taxes due.
@dbisht53
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