This is the same for friends in Europe, who, when using US accounts, have the in-game store in Euro, the local currency, while the web store is in US Dollars, and for friends on US accounts in Australia (which are the only ones available to Australian players), who have the in-game store in Australian Dollars, but the web store in US Dollars.
Why is it a problem? Well, these things are a lot more expensive in Euro or £ pricing than in US$. If you can read the currencies on the in-game store and the web store, if I used the in-game store I'd pay $7.40 for a discounted pet as opposed to $5. The Alterac Brew Pup costs me $13 on the in-game store, or $10 on the web store. The Fey Dragon costs me $36 on the in-game store, or $25 on the web store.
The moral of the story is that, until Blizzard fixes the in-game store to match the game region, use the web store for your US-region purchases!