All I/O pins are isolated from the world by at least a 10K resistor in series with the pins. Inputs are pulled up to +5 volts, grounded for input. All outputs that go to the power section are isolated by at least 10K in series with a buffer transistor or an op amp. The power section is still only 18 to 20 volts DC, but can provide as much as 15 amps...with only a 2.5 amp load during debug.
Sounds like you've got ground bounce, high current not finding an easy path home, so it takes whatever path it can find.
Depending on the scope, it may or may not be observable.
Try running the high power part from an independent supply, with only a 1 ohm resistor connecting it to the uP's ground.
Isolate any external connections on the high power system, so that they don't connect to any other "ground".