Oscilloscope reading

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P.S. 50 Ohm scope termination or other specified, plays a crucial role depending on the source's output impedance so to see square shapes in their real nature at point of probing. Maybe an RG 58 with naked tip and short shield to probe signal & near GND, also a 50 Ohm across at the BNC end.
 
I think much of your problems comes from the pcb and circuit layout. You should also use a needle for the ground instead of a wire. This is really important in order to have a low ground inductance.
 

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