So i filed my tax return and got the fee included in my tax return i filed. I recieved tax return after you guys charged me for the 59.99$ fee.I am now owed 59.99$?

You will need to talk with customer support for this:

To call TurboTax customer support

https://ttlc.intuit.com/questions/1899263-what-is-the-turbotax-phone-number

They are available from 5 a.m. to 5 p.m. Pacific time Monday - Friday.

Or does this explain what you are experiencing?

I assume you chose to pay the TurboTax product fees out of your Federal refund.   Was your Federal refund delayed by the IRS for an unusual length of time, and did TurboTax send you a bill for the 59.99 in fees, which you paid?   If so, then when your refund finally came through, the product fee of 59.99 should not have been deducted again.   However, it may have charged you the 39.99 service fee for using that payment method.

In any case, if you need to discuss any fee situation with TurboTax Support, use the method that xmasbaby0 left you above.