Program: 31471
Project: 31471
Buggy source:
private static boolean transferRecipe(@Nonnull RecipeLayout recipeLayout,@Nonnull EntityPlayer player,boolean doTransfer){
  Container container=player.openContainer;
  IRecipeTransferHelper transferHelper=JEIManager.recipeRegistry.getRecipeTransferHelper(container,recipeLayout.getRecipeCategory());
  if (transferHelper == null) {
    return false;
  }
  Map<Integer,Slot> inventorySlots=new HashMap<>();
  for (  Slot slot : transferHelper.getInventorySlots(container)) {
    inventorySlots.put(slot.slotNumber,slot);
  }
  Map<Integer,Slot> craftingSlots=new HashMap<>();
  for (  Slot slot : transferHelper.getRecipeSlots(container)) {
    craftingSlots.put(slot.slotNumber,slot);
  }
  IRecipeWrapper recipeWrapper=recipeLayout.getRecipeWrapper();
  if (recipeWrapper.getInputs().size() > craftingSlots.size()) {
    return false;
  }
  GuiItemStackGroup itemStackGroup=recipeLayout.getItemStacks();
  List<List<ItemStack>> requiredStackLists=getInputStacks(itemStackGroup.getGuiIngredients());
  List<ItemStack> availableItemStacks=new ArrayList<>();
  int filledCraftSlotCount=0;
  int emptySlotCount=0;
  for (  Slot slot : craftingSlots.values()) {
    if (slot.getHasStack()) {
      if (!slot.canTakeStack(player)) {
        return false;
      }
      filledCraftSlotCount++;
      availableItemStacks.add(slot.getStack());
    }
  }
  for (  Slot slot : inventorySlots.values()) {
    if (slot.getHasStack()) {
      availableItemStacks.add(slot.getStack());
    }
 else {
      emptySlotCount++;
    }
  }
  if (filledCraftSlotCount - recipeWrapper.getInputs().size() > emptySlotCount) {
    return false;
  }
  List<ItemStack> matchingStacks=getMatchingItems(availableItemStacks,requiredStackLists);
  if (matchingStacks == null) {
    return false;
  }
  Map<Integer,ItemStack> slotMap=buildSlotMap(itemStackGroup,matchingStacks);
  if (slotMap == null || StackUtil.containsSets(slotMap.values(),availableItemStacks) == null) {
    return false;
  }
  for (  Map.Entry<Integer,ItemStack> entry : slotMap.entrySet()) {
    int slotIndex=entry.getKey();
    if (slotIndex >= container.inventorySlots.size()) {
      return false;
    }
    Slot slot=container.getSlot(slotIndex);
    ItemStack stack=entry.getValue();
    if (slot == null || !slot.isItemValid(stack)) {
      return false;
    }
  }
  if (doTransfer) {
    PacketRecipeTransfer packet=new PacketRecipeTransfer(slotMap,craftingSlots.keySet(),inventorySlots.keySet());
    JustEnoughItems.common.sendPacketToServer(packet);
  }
  return true;
}

Fixed version (ground truth):
private static boolean transferRecipe(@Nonnull RecipeLayout recipeLayout,@Nonnull EntityPlayer player,boolean doTransfer){
  Container container=player.openContainer;
  IRecipeTransferHelper transferHelper=JEIManager.recipeRegistry.getRecipeTransferHelper(container,recipeLayout.getRecipeCategory());
  if (transferHelper == null) {
    return false;
  }
  Map<Integer,Slot> inventorySlots=new HashMap<>();
  for (  Slot slot : transferHelper.getInventorySlots(container)) {
    inventorySlots.put(slot.slotNumber,slot);
  }
  Map<Integer,Slot> craftingSlots=new HashMap<>();
  for (  Slot slot : transferHelper.getRecipeSlots(container)) {
    craftingSlots.put(slot.slotNumber,slot);
  }
  IRecipeWrapper recipeWrapper=recipeLayout.getRecipeWrapper();
  if (recipeWrapper.getInputs().size() > craftingSlots.size()) {
    return false;
  }
  GuiItemStackGroup itemStackGroup=recipeLayout.getItemStacks();
  List<List<ItemStack>> requiredStackLists=getInputStacks(itemStackGroup.getGuiIngredients());
  List<ItemStack> availableItemStacks=new ArrayList<>();
  int filledCraftSlotCount=0;
  int emptySlotCount=0;
  for (  Slot slot : craftingSlots.values()) {
    if (slot.getHasStack()) {
      if (!slot.canTakeStack(player)) {
        return false;
      }
      filledCraftSlotCount++;
      availableItemStacks.add(slot.getStack());
    }
  }
  for (  Slot slot : inventorySlots.values()) {
    if (slot.getHasStack()) {
      availableItemStacks.add(slot.getStack());
    }
 else {
      emptySlotCount++;
    }
  }
  if (filledCraftSlotCount - recipeWrapper.getInputs().size() > emptySlotCount) {
    return false;
  }
  List<ItemStack> matchingStacks=getMatchingItems(availableItemStacks,requiredStackLists);
  if (matchingStacks == null) {
    return false;
  }
  Map<Integer,ItemStack> slotMap=buildSlotMap(itemStackGroup,matchingStacks);
  if (slotMap == null || StackUtil.containsSets(slotMap.values(),availableItemStacks) == null) {
    return false;
  }
  List<Integer> craftingSlotIndexes=new ArrayList<>(craftingSlots.keySet());
  Collections.sort(craftingSlotIndexes);
  List<Integer> inventorySlotIndexes=new ArrayList<>(inventorySlots.keySet());
  Collections.sort(inventorySlotIndexes);
  for (  Map.Entry<Integer,ItemStack> entry : slotMap.entrySet()) {
    int craftNumber=entry.getKey();
    int slotNumber=craftingSlotIndexes.get(craftNumber);
    if (slotNumber >= container.inventorySlots.size()) {
      return false;
    }
    Slot slot=container.getSlot(slotNumber);
    ItemStack stack=entry.getValue();
    if (slot == null || !slot.isItemValid(stack)) {
      return false;
    }
  }
  if (doTransfer) {
    PacketRecipeTransfer packet=new PacketRecipeTransfer(slotMap,craftingSlotIndexes,inventorySlotIndexes);
    JustEnoughItems.common.sendPacketToServer(packet);
  }
  return true;
}