If your employer pays more than the $5250 tax-free amount of tuition on your behalf, the excess must be added to your W-2 at the end of the year, and is subject to income tax and social security/medicare tax. Whether you get a refund depends on your overall income, dependents, deductions, credits, and withholding.
Since you paid part of your tuition with taxable money, that part is eligible for the American Opportunity Credit or the Lifetime Learning credit, depending on the other eligibility rules. (Basically, it is treated the same as if your employer gave you a raise and you paid the tuition yourself -- since you paid it partly with taxable money, that part is eligible for credits.)