You got charged 3 bucks for the game coz thats what the game costs in appstore right now. http://appshopper.com/games/dark
You are able to dispute the charge when the email arrives detailing your purchase. Simply go into the purchase interface - there should be something akin to "dispute charge" or something there, IIRC. EDIT: Remember, this is entirely at Apple's discretion, so it would do you good to swiftly delete said app and announce your desire for said refund.
It's been $3 for eleven days now. Judging by the timing of your post/arrival of your receipt and estimating the date you made the purchase... I'd say it was probably $3. He wasn't patronizing you anyway, he was giving you the answer. Regardless of whether or not there was an error on Apple's part, the reason you got charged that amount is because Apple think that's what the game costs. You freakin' asked.
If there was a reputation system I would totally give you +1 reputation. Not to rain on your parade, but there have been many others that have been overcharcpged, and there are also others for getting charged for in-app purchases they have never made (Kingdom Conquest). Many, many people in the iTunes rating system have talked about this, and I have lost $40.00 in my US iTunes account for no apparent reason, I did not even know about this application, luckily I didn't link a credit card to my account. @TheBatOuttaHell That's 37 games lost....but I already spent about $400 in iTunes with my own money, with $100 going in Eliminate Pro. By the way, at the time, I didn't have a Xbox 360.
Um, tell them to bring it up to Apple? Apple have never refused me a refund, and return the lost credit within three business days tops every single time. If you're not keeping up with your own credit card record and didn't know you lost any money, then clearly, that's your fault. I've poured over $2,000 into the AppStore, more than games for every other console I own combined. However, I still go through my iTunes receipts at the end of each month and keep track. Hell yes it was.