VNH5019A Flyback issue on custom PCB
I'm not experienced with using scopes. I have a single probe connected
  to channel one. This probe has a ground alligator clip. This I clipped
  to a ground standoff on the pcb.


That forms a small loop antenna suitable for picking up magnetic field impulses and it is highly likely that what you are seeing is a phantom. The currents in your circuit are around 10 amps (and with quite fast edges) and this type of scope probing problem is commonplace to find on switching converters. You do need to use a ground plane and proper probing on a circuit like this or you'll be fighting an uphill battle.

Here's something you can try. Connect the alligator clip to the scope probe end to form a short. Now connect the scope probe (with intact alligator clip) to the grounding post on your circuit. What would you expect to see and what do you actually see?