Did they ever explain why it only costs 99 cents?

No.

the meat costed them 40c a pound, that says a lot.

cause the way they process the meat is unclean , it has crap in it, they add preservatives , they add chemicals that make the meat inflate making it seem like more meat , all that ends up being cheap , so if they sell it cheap they make more money.

Great point about the use of editing for trailers that are misleading.
For info on why the burgers are so cheap, trying reading the book "Fast Food Nation." Or watch/read "Food, Inc."

With them purchasing meat at 40 cents a pound, and selling their burgers at a typical 2 oz regular hamburger, and a 4 oz bigger sized hamburger, that generates enormous profit. If one 2 oz burger sells for 99 cents (about $1.06 after tax), and there are 16 ounces in a pound, that's 8 of those 2 oz burgers per pound, generating $8.48 per pound.

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its not 100% meat. they add filler AKA "pink goo" so there is not that much real meat in each patty. Thats why its so cheap.

I just finished watching the film and I think you might have mistaken something here. They never said what the Big one cost. The only time they stated that a burger cost .99 cents was when the Mickey's grill cook was talking to another one of the workers and they mentioned another restaurant and said something about their burger and how it was not as good. Then they mentioned that it was only .99 cents. This was never about The Big One or any of the burgers at that restaurant.