I transferred between divisions of the same company. I received two w-2's, and the company withheld too much social security tax. My electronic refund was rejected because I have two w-2's with same company ID. If I combine my W-2's together, the software says the company owes me the excess social security tax. The company says the government. Who is right?

If you work for 2 different employers and have too much SS tax withheld (more than $6621.60 for the year) you can claim a credit on line 69 of your 1040. But if the excess was withheld by employer error (which is what this sounds like, assuming your W2's shows the same employer EIN), you can not take the credit, but must instead get a refund from your employer. If your employer refuses to do so, you can file form 843 to request a refund from the government. See page 263 of: http://www.irs.gov/pub/irs-pdf/p17.pdf