Q.  Is there anyway to get this taxes refunded when I file the tax return next year? 

A. No and yes. Job related education is not deductible by a W-2 employee.  So you cannot take a deduction or reclassify this money as tax free on your tax return.  Even when (before 2018) job expenses (including education) were deductible, they were only an itemized deduction subject to a 2% of AGI threshold.  

However, since you are effectively  paying the tuition with "your own" after tax money, you are eligible for the Lifetime Learning Credit (LLC). The LLC is 20% of tuition paid, so there's a chance you'll get most of it back. 

As others have said, the only way to correct this is for your employer to treat the money as tax free, on the W-2.  This is essentially between you and you're employer, not you and the IRS.  You said "I contacted HR and they said once the application is processed, they cannot fix it".  If you can't convince them to change the tax treatment of the payments, going forward, you're simple out of luck . 

The tax law is basically that job related education is not deductible by a W-2 employee.  But, job related education provided by the employer is deductible by the employer (and tax free to the employee).  They just have to do the paper work correctly.