When that happens, the first thing you have to do is select the element and check for margins, padding, or position values. Then if you find nothing, select the parent (up arrow) and do the same. And repeat until you find a property that's in the way of your design. If you hover the margin/padding arrows you highlight the margin or padding, so it's quite easy to debug.
Here for the method It's actually the very same method you use when you inspect a page in the browser inspector, you select and element and check the properties, and go up, or down, in the hierarchy.
Press "?" for the keyboard shortcuts. Check how to use the arrow keys to navigate into the hierarchy. There's also the hierarchy at the bottom of the screen. Those two are your best friends