Program: 169665
Project: 169665
Buggy source:
@Override public boolean onMultiTileActivated(IMultiTile tile,EntityPlayer player,int side,IPos3D hit){
  if (isServer()) {
    Pos pos=new Pos((TileEntity)tile).sub(xi(),yi(),zi());
    if (getLayoutOfMultiBlock().containsKey(pos)) {
      if (getMissile() != null) {
        IModule module=null;
        if (player.getHeldItem() != null)         module=((IModuleItem)player.getHeldItem().getItem()).getModule(player.getHeldItem());
        if (isWarheadSide(pos)) {
          if (module == null) {
            if (getMissile().getWarhead() != null) {
              ItemStack stack=getMissile().getWarhead().toStack();
              player.inventory.setInventorySlotContents(player.inventory.currentItem,stack);
              getMissile().setWarhead(null);
              updateMissileItem();
              player.inventoryContainer.detectAndSendChanges();
            }
          }
 else           if (module instanceof Warhead) {
            if (missile.getWarhead() == null) {
              getMissile().setWarhead((Warhead)module);
              reducePlayerHeldItem(player);
              updateMissileItem();
            }
 else {
              player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
            }
          }
 else {
            player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
          }
        }
 else {
          if (module == null) {
            if (getMissile().getEngine() != null) {
              ItemStack stack=getMissile().getEngine().toStack();
              player.inventory.setInventorySlotContents(player.inventory.currentItem,stack);
              getMissile().setEngine(null);
              updateMissileItem();
              player.inventoryContainer.detectAndSendChanges();
            }
          }
 else           if (module instanceof RocketEngine) {
            if (missile.getEngine() == null) {
              getMissile().setEngine((RocketEngine)module);
              reducePlayerHeldItem(player);
              updateMissileItem();
            }
 else {
              player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
            }
          }
 else {
            player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
          }
        }
      }
 else       if (player.getHeldItem() != null) {
        return onPlayerRightClick(player,side,new Pos(hit));
      }
    }
  }
  return true;
}

Fixed version (ground truth):
@Override public boolean onMultiTileActivated(IMultiTile tile,EntityPlayer player,int side,IPos3D hit){
  if (isServer()) {
    Pos pos=new Pos((TileEntity)tile).sub(xi(),yi(),zi());
    if (getLayoutOfMultiBlock().containsKey(pos)) {
      if (getMissile() != null && player.getHeldItem().getItem() instanceof IModule) {
        IModule module=null;
        if (player.getHeldItem() != null)         module=((IModuleItem)player.getHeldItem().getItem()).getModule(player.getHeldItem());
        if (isWarheadSide(pos)) {
          if (module == null) {
            if (getMissile().getWarhead() != null) {
              ItemStack stack=getMissile().getWarhead().toStack();
              player.inventory.setInventorySlotContents(player.inventory.currentItem,stack);
              getMissile().setWarhead(null);
              updateMissileItem();
              player.inventoryContainer.detectAndSendChanges();
            }
          }
 else           if (module instanceof Warhead) {
            if (missile.getWarhead() == null) {
              getMissile().setWarhead((Warhead)module);
              reducePlayerHeldItem(player);
              updateMissileItem();
            }
 else {
              player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
            }
          }
 else {
            player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
          }
        }
 else {
          if (module == null) {
            if (getMissile().getEngine() != null) {
              ItemStack stack=getMissile().getEngine().toStack();
              player.inventory.setInventorySlotContents(player.inventory.currentItem,stack);
              getMissile().setEngine(null);
              updateMissileItem();
              player.inventoryContainer.detectAndSendChanges();
            }
          }
 else           if (module instanceof RocketEngine) {
            if (missile.getEngine() == null) {
              getMissile().setEngine((RocketEngine)module);
              reducePlayerHeldItem(player);
              updateMissileItem();
            }
 else {
              player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
            }
          }
 else {
            player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
          }
        }
      }
 else       if (player.getHeldItem() != null) {
        return onPlayerRightClick(player,side,new Pos(hit));
      }
    }
  }
  return true;
}