To answer the OP's question, as others have said, no that isn't right, it s/b flush. But I'm not sure he needs to take it back. He probably just needs to open/remove the cover and reseat it.
I love the Magic Mouse but quite frankly the battery cover leaves something to be desired. I purchased a Magic Mouse the day after they came out and have replaced the batteries a couple of times. Each time it's been a bit of a struggle to get the battery compartment cover open initially and then to re-seat it flush w/the rest of the case properly. Apple engineering is usually top-notch, but this time they missed the target. Once it's seated it's fine, but it does not easily open or close.