I recently bought a new boat and noticed some electrolysis on the minn kota trolling motor. The trolling motor is the only think wired to the trolling motor batteries. Everything else is wired to the 12v cranking battery. I’ve been finding some conflicting information online. Do I need to have a common ground between the trolling motor system and the cranking battery? Or should they stay isolated? Not sure if it matters, but all 3 batteries are wired to a Bass Pro Shops 3 bank charger. Thanks for your help.

Electrolysis on the trolling motor? Where? Everything external on the motors is composite. Did you call Minn Kota? If not, that's where I would start. 

Sometimes it can be from the charger if there is a ground crossover. Also did anyone add electronics that are connected to the TM and possibly didn’t wire the ground  correctly. Clean everything up and then disconnect the charger from the cranking battery when not charging and see if that helps. 
But what @slonezp said I would try first.

also check if the charger is mounted directly to the boat (assuming aluminum boat).  If it is, get a piece of starboard or similar to separate them.

Picture? 

Where do you see corrosion oxides? 

Tom

What you are seeing is probably just common oxidation and corrosion.  Especially if the motor has ever been used in brackish water.

As for the ground, you do not need to make a common ground between the TM and cranking battery.  Each one is their own independent system.  If it's an aluminum boat, DO NOT connect any ground wires to any part of the aluminum hull.