The assumption that the master is better in everything because he is the master is false. The master is better in the relevant aspects of his craft. There is no need to weaken him, simply make the pair face challenges a bit outside the craft.
A master witcher will be better with the sword and will know more about monsters and magic, but being feared and called a mutant tends to hamper normal social interaction quite a bit. Also, while Witcher schools tend to teach the same "curriculum" to their students, depending on the backstory of the characters the trainee might have had a different focus than his master (master is great at Signs, trainee is very good at Alchemy etc.) Or the trainee could have picked up skills before he has gone to school, and depending on those he could have fields where he outstrips his master.
In the usual threetrio of Combat-Social-Intellectual challenge, the master will be better in two, but it is believable, that the apprentice has an edge in the third. Build it in during character creation, and you have a dynamic, if (if mismatched) duo where one won't outshine the othersother.
On your specific example: Witchers are generally social outcasts, and a pre-Trial trainee, — one who doesn't show signs of mutations — could get a lot of knowledge out of the locals that his master won't. Or he could gather a lot of intel which would be hidden from a true witcher until the end. Like, like the fact the villagers don't have the money to pay for their services.