Most of this is irrelevant. Ask for you money back. You don't need to provide Apple any more excuse than "something went wrong, and I ended up paying for an app I thought was free."
But, regardless how things went down, and we can debate possible glitches, possible missteps, and how things work all day and get nowhere, here are some simple facts that you should know before deciding that the GoodReader people are cons.
One. They have no control over how the store works. None. They can set a price. After that all processing is done by Apple. There is no way GoodReader could set up a bait and switch intentionally. Maybe, possibly, they had the app on sale and you got caught as they took it off sale. I don't think this is likely. The volume of App Store purchases means that if people were being caught this way it would be hundreds or even thousands, and the complaint would roll in.
Two. GoodReader has been in the App Store almost as long as there has been an App Store. They have a solid reputation and no need to stoop to bait and switch tactics. It would only harm what is a good, long-term business for them. The likely hood that they would, even if the could, play stupid games with the App Store is vanishingly small.
And a half. Any pricing snafu during purchase would be entirely Apples fault; which puts us back at asking Apple for the refund. Though since they take it from the developer's account, it hardly hurts them. They keep their 30% too, so it cost the developer big time if lots of refund requests come in.
My conclusion (for what it is worth) is that whatever happened was an accident. Who or how it was caused is irrelevant at this point. The chances of it being intentional are very small. Machine, man, or murphy; it's done.