OK about the LEDs.
Regarding the push buttons (and any other I/O port in general). This isn't actually a bug. It's by design. In order to avoid something like that, please arrange the buttons in reverse order. All ports are rendered in the same order they are created.So by reversing their order, you can hide their label behind the newer port.
Putting the label on the left side of the button will not look good in case the button has a large name. Sorry about that :)