1. The "remove breakpoint" button (X) isn't aligned vertically.
2. The "remove breakpoint" button (X) isn't aligned with the checkbox above it.
3. When breakpoints are added, the "Breakpoint" title bar gets a height larger than the others – see "Call Stack", for example. (I'm almost sure this happens because of the checkbox on the right side.)

Screenshot

In vertical mode, the problem described in the 3rd item gets even more evident:

Notice the height difference between the title bars.