See attached screenshot. This can be reproduced by placing the Downloads button on the tab strip or the rightmost slot in the toolbar and then maximizing the application window. Other OS X applications with similar doorhanger popups solve this by creating the popup with a different orientation. In this case I don't think we want the panel to cover chrome, so moving the arrow closer to the border of the panel should be a viable fix. I'm not sure whether this is a Downloads panel or Theme bug, please reassign if needed.