I think the navigation system was OK, we just said the impacts were further West than they actually were so the V2s fell on East London instead
The British noticed that V1s aimed at London tended to fall a little short. This would have been to the South and East of London since that's the direction they were coming from. They reported more hits on the North West of the city, expecting correctly that Nazi spies in Britain would let the Luftwaffe know about this.
So the range was decremented further, meaning even more hits on the southern and eastern suburbs, but statistically fewer people killed and buildings destroyed as the mean moved to less populated areas.