Most (if not all) tickets are sold via a GDS like Amadeus or Sabre. Autopricing is when the GDS automatically calculates the total ticket price. If a travel agent sells a ticket that 'autopriced', the GDS guarantees that it is a valid price and the TA cannot receive a debit memo saying they owe more money.

I see that sentence in nearly every set of fare rules. I think it's CYA boilerplate language. Best guess, it means that the words printed in the rules govern the fare, even if there is a mistake in the way the ticket data was entered into the GDS system by the airline.