Hers was a coding problem, not an in-game physical issue: Felix fixes stuff that's broken in-game (regardless of which game), but coding issues need to be fixed by going into the base code itself and mucking about (or resetting the program, but that's still not an in-game solution).
Also, while angrily muttering to himself at one point, Ralph does mention that Felix got his "magic hammer" from his father (I forget if he said "given" or "inherited", tho). That could just be programmed backstory like Calhoun's fiance, or the existence of a Fix-It, Felix game about Felix Sr. could have been left unexplored to free up sequel possibilities (this film's theme was all about "you are who you are", so a sequel could be about knowing where you come from - beyond the coding, thus further exploring the "become more than your programming" idea).