An error like that? Trust me they already know. Being a pre-order they could chose to bill you the full amount on the day of release and would be legally entitled to do so, saying that the 44 cent was just a 1% charge to insure the card was valid.
Honestly if it happened they weekend they'll probably deal with it on Monday, if not they're most likely trying to decide if it's worth it to them to charge the full amount (which they may not bother if few enough people purchased it).
Being a pre-order they can refund it at any time before release as you haven't actually received anything yet.
This is of course assuming that 44 cents was only what you were billed and it wasn't the "advertised price" at the time.
Actually I made the transaction on Friday, and then checked my online bank account this evening.
The service is Gamersgate, by the way.
I'm positive it isn't an initial charge. I didn't even purchase the game directly, I purchased 40$ in blue coins, which I then used in conjonction with the blue coins tied to my account towards the pre-order.
I also pre-ordered both Alpha Protocol and Red Faction Guerilla on the same site, and on both occasions, I was billed the full amount right when the transaction was over, in spite of both games not being released at the time of purchase.