Alignment issues are usually the result of objects lying outside the layout. This issue is most commonly seen when you copy contents from a layout with larger dimensions to one that are smaller. For example, when you copy and paste contents from a desktop to a mobile layout, chances are that some objects are placed outside the layout. They are especially invisible if you have disabled Frame Edges.
When you publish a layout with such objects, the browser includes the space containing the objects outside the layout. The extra space makes your page look smaller and incorrectly aligned.