You are correct you should not be getting 12v at the brake wire when disconnected. My guess is something was hooked up incorrectly when the truck was worked on. which brings up two questions.
What was the fix on the truck? Was the turn signal or brakelight switch replaced?
Is your brake controller using a manufactured cable to connect to the truck wiring? Or is it just scotchlocked onto existing under dash wiring?
I'm thinking the guy that did the repairs probably hooked the blue wire up to the wrong side of the brake light switch.