Sounds to me like...
You're gripping the gun wrong.
If your left thumb knuckle is being punished and you're left handed you're probably gripping the gun in a fashion so you can get more of your finger on the trigger. Do you have just the first section of your finger on the trigger or do you have the crook of the finger on it... or worse yet part of the second section of your finger too?
I found a long while ago that I was doing that and the gun was hurting my knuckle too... only it was my right knuckle because I'm right handed.
This is who we are, what we do.