I received 10K for relocation when I started with a company. I agreed to work for 24 months in exchange for this. However, after taxes were taken out, I only received 6500. Now after 8 months I am leaving the company. They would like 6600 hundred in return. The agreement was for a prorated amount to be paid back for each month that I had not completed. Am I being double taxed on this?
Shouldn't I pay 4300?

You will either have to amend the tax return to reflect the actual amount of the bonus earned, or claimed as a miscellaneous deduction that amount of the bonus returned on your current year tax return.