I have paid for my TurboTax fees in the past using direct deposit and have never had to pay a $40 processing fee. Why do I have to this time?

If you choose to pay your TurboTax fees by having them deducted from your federal refund there is a refund processing fee of $39.99 ($44.99 in CA) which has been in effect for years.  You can avoid the fee by paying your fees upfront using a credit/debit card.

REMOVE REFUND PROCESSING FEE

https://ttlc.intuit.com/questions/1900517-how-do-i-remove-refund-processing-fees-in-turbotax-online-and-change-my-payment-method