I paid extra to have my payment for my refund directly taken from my refund but I later had my refund garnished by the government, but I still had to pay the full amount.

Yes?  What is your question?  

They only get the fee deducted AFTER the IRS sends it.  So if the IRS kept it Turbo Tax couldn’t take the fee out.  At least you will be saving the extra 39.99 Refund Processing Service charge (44.99 in California).

See What if the IRS reduces my Refund

  https://ttlc.intuit.com/questions/2552376-what-if-my-federal-refund-isn-t-enough-to-cover-my-turbotax-fees  

My question is why did I have to pay extra to take my payment out of my refund when the payment was taken out of my checking account after my refund was garnished?

I said why.  Turbo Tax only gets their fee AFTER the IRS sends it.  So if the IRS keeps your refund then Turbo Tax does not get paid.  And you still owe the fees.

Ok. I paid for something I’m not getting. Not using Turbo Tax again.

Why was your refund garnished?  That's not Turbo Tax fault.  Any other tax program would be the same way.

I know but what I’m saying is I paid the extra $40 to have my payment deducted from my refund, it got garnished, but I still have to pay the extra $40 when it was taken out of my checking account, not my refund.