Thanks for the answers HansV and Nate. Part of the confusion I had was when I was using the 'standard' connectors (orange/striped orange and purple/striped purple). I wasn't sure if the negative connector was placed at the most negative point on the board or at ground.
From the videos and feedback it seems that this connector should be placed at ground to avoid a short.
My set up has a laptop , powered by an AC/DC adapter with a ground reference, connected to the Discovery 2. The Discovery 2 is powered by an adapter with a floating reference, and a PCB board is connected to an AC/DC adapter with a ground reference.
So as long as the negative reference (striped orange / striped purple) of the oscilloscope is attached to ground on the PCB board everything is ok.
Thanks guys for improving my understanding