Program: 79871
Project: 79871
Buggy source:
@Override public void randomizePokemonTypes(boolean evolutionSanity){
  if (evolutionSanity) {
    Set<Pokemon> dontCopyPokes=RomFunctions.getBasicOrNoCopyPokemon(this);
    for (    Pokemon pk : dontCopyPokes) {
      pk.primaryType=randomType();
      pk.secondaryType=null;
      if (pk.evolutionsFrom.size() > 0) {
        if (this.random.nextDouble() < 0.35) {
          pk.secondaryType=randomType();
          while (pk.secondaryType == pk.primaryType) {
            pk.secondaryType=randomType();
          }
        }
      }
 else {
        if (this.random.nextDouble() < 0.5) {
          pk.secondaryType=randomType();
          while (pk.secondaryType == pk.primaryType) {
            pk.secondaryType=randomType();
          }
        }
      }
    }
    Set<Pokemon> firstEvos=RomFunctions.getMiddleEvolutions(this);
    for (    Pokemon pk : firstEvos) {
      Pokemon evolvedFrom=pk.evolutionsTo.get(0).from;
      pk.primaryType=evolvedFrom.primaryType;
      pk.secondaryType=evolvedFrom.secondaryType;
      if (pk.secondaryType == null) {
        if (this.random.nextDouble() < 0.15) {
          pk.secondaryType=randomType();
          while (pk.secondaryType == pk.primaryType) {
            pk.secondaryType=randomType();
          }
        }
      }
    }
    Set<Pokemon> secondEvos=RomFunctions.getFinalEvolutions(this);
    for (    Pokemon pk : secondEvos) {
      Pokemon evolvedFrom=pk.evolutionsTo.get(0).from;
      pk.primaryType=evolvedFrom.primaryType;
      pk.secondaryType=evolvedFrom.secondaryType;
      if (pk.secondaryType == null) {
        if (this.random.nextDouble() < 0.25) {
          pk.secondaryType=randomType();
          while (pk.secondaryType == pk.primaryType) {
            pk.secondaryType=randomType();
          }
        }
      }
    }
  }
 else {
    List<Pokemon> allPokes=this.getPokemon();
    for (    Pokemon pkmn : allPokes) {
      if (pkmn != null) {
        pkmn.primaryType=randomType();
        pkmn.secondaryType=null;
        if (this.random.nextDouble() < 0.5) {
          pkmn.secondaryType=randomType();
          while (pkmn.secondaryType == pkmn.primaryType) {
            pkmn.secondaryType=randomType();
          }
        }
      }
    }
  }
}

Fixed version (ground truth):
@Override public void randomizePokemonTypes(boolean evolutionSanity){
  List<Pokemon> allPokes=this.getPokemon();
  if (evolutionSanity) {
    for (    Pokemon pk : allPokes) {
      if (pk != null) {
        pk.temporaryFlag=false;
      }
    }
    Set<Pokemon> dontCopyPokes=RomFunctions.getBasicOrNoCopyPokemon(this);
    for (    Pokemon pk : dontCopyPokes) {
      pk.primaryType=randomType();
      pk.secondaryType=null;
      if (pk.evolutionsFrom.size() == 1 && pk.evolutionsFrom.get(0).carryStats) {
        if (this.random.nextDouble() < 0.35) {
          pk.secondaryType=randomType();
          while (pk.secondaryType == pk.primaryType) {
            pk.secondaryType=randomType();
          }
        }
      }
 else {
        if (this.random.nextDouble() < 0.5) {
          pk.secondaryType=randomType();
          while (pk.secondaryType == pk.primaryType) {
            pk.secondaryType=randomType();
          }
        }
      }
      pk.temporaryFlag=true;
    }
    Set<Pokemon> middleEvos=RomFunctions.getMiddleEvolutions(this);
    for (    Pokemon pk : allPokes) {
      if (pk != null && !pk.temporaryFlag) {
        Stack<Evolution> currentStack=new Stack<Evolution>();
        Evolution ev=pk.evolutionsTo.get(0);
        while (!ev.from.temporaryFlag) {
          currentStack.push(ev);
          ev=ev.from.evolutionsTo.get(0);
        }
        while (true) {
          Pokemon to=ev.to;
          Pokemon from=ev.from;
          to.primaryType=from.primaryType;
          to.secondaryType=from.secondaryType;
          if (to.secondaryType == null) {
            double chance=middleEvos.contains(to) ? 0.15 : 0.25;
            if (this.random.nextDouble() < chance) {
              to.secondaryType=randomType();
              while (to.secondaryType == to.primaryType) {
                to.secondaryType=randomType();
              }
            }
          }
          to.temporaryFlag=true;
          if (currentStack.isEmpty()) {
            break;
          }
 else {
            ev=currentStack.pop();
          }
        }
      }
    }
  }
 else {
    for (    Pokemon pkmn : allPokes) {
      if (pkmn != null) {
        pkmn.primaryType=randomType();
        pkmn.secondaryType=null;
        if (this.random.nextDouble() < 0.5) {
          pkmn.secondaryType=randomType();
          while (pkmn.secondaryType == pkmn.primaryType) {
            pkmn.secondaryType=randomType();
          }
        }
      }
    }
  }
}