When there were scoring problems at my son's games they were associated with substitutions that were probably not sufficiently communicated to the scorer (in one instance there were consecutive pinch hitters and then a pinch runner for one of the hitters...this caused the rest of the inning to get out of synch). I think that part of the solution is that the coaches and umpire have to take the time to make sure that substitutions are clearly communicated and deal with the fact that this will slow the game down just a bit.