Tax question - doesn't seem right. Wife's W2 gross pay was $3300, but they only took out $6.84 for federal tax

What exactly are you looking for? They are right that what is done is done. You got to hold on to more of your money all year and should be happy.If she will be working at this employer again, change her to zero allowances on federal and she will have more withheld. Maybe that is what happened with the other jobs.