I’ve marked this topic as no-bug, because I think that this is just how it works and it’s not Bricks related.
When you click on the menu item in the page, it just scrolls you down and aligns the top of the page with the anchor.
But, when you open the header menu via hamburger button, the menu pushes the whole website down. So when you click on the anchor link, here is what happens:
browser correctly aligns the top of the page (which now contains the menu) to the anchor
the menu is closed
the whole page is moved up (to fill the place where the menu was visible before)
visually, it appears that the browser did not aligned the anchor correctly, but in fact it did, it’s just that the page content changed.