All my inner flaps on M/L and Reissues are able to close. I usually left them undone when I'm using them since I don't like to press down on my flaps and its cumbersome to access. But I usually store them buttoned when I don't use them.
There must be something wrong with the button if you are unable to close it even after pressing it down. Although the button serves no purpose for me, I would still return or exchange the bag since its brand new and it should not come with a faulty part.