There are many reason this could happen.  Your student loan interest is an adjustment to income.  This adjustment could have changed any number of your income based credits.

This still doesn't seem accurate to me. We are taking the standard deduction of $24k married filing joint. We didn't have any other income credits. So it just seems odd that putting in this interest paid of $6k would lower our refund amount by $600.  It pops up saying congrats on your $2500 income credit, and then takes $600 off our refund.  So we are out the 6K in interest paid AND $600 of our refund. Do I have to claim the interest that I paid and my student loans? 

You stated that you are receiving the Earned Income Credit, that could be a pretty big jump depending on where you are hitting. Here is the link to the EIC tables  so you can check for yourself. EIC begins on page 16.

As for claiming the student loan interest, because of my legal credentials, I am required to inform you that you should claim the  interest paid. 

I am not sure where I gave the impression that we were getting an EIC... We are not.  Please re-read my question. I really need to know if this a glitch in the program or if claiming student loan interest lowers your tax refund when it is said to be a tax credit? I am confused. 

I would review your input.  It almost sounds like the $6,000 was treated as income instead of an adjustment to income.

The input for the student loan interest would go under the Federal section.

1. Select "Deductions & Credits"
2. Select "Education"
3. Select "Student Loan Interest Paid (Form 1098-E).

Continue to enter the information here to enter your student interest.  

Your deduction could be limited by AGI limits as listed below:

Attached is additional information for your reference.

Student loan interest deduction