Sorry for slow reply, always so busy with work. 
Okay, may have been wrong to think it was Forge. I don't know why but it seems in RecipesTools.java the recipe was incorrect on Line 5 
private String[][] recipePatterns = new String[][] {{"XXX", " # ", " # "}, {"X", "#", "#"}, {"XX", "X#", " #"}, {"XX", " #", " #"}}; 
  
Recipe 0 = Picaxe 
Recipe 1 = Shovel 
Recipe 2 = Hatchet 
Recipe 3 = Hoe 
  
The recipes are missing spaces and should look like this: 
private String[][] recipePatterns = new String[][] {{"XXX", " # ", " # "}, {"X", "#", "#"}, {"XX ", "X# ", " # "}, {"XX ", " # ", " # "}}; 
  
This fixed my issue when CraftingManager called for these recipes and it ended up making them an ItemStack[6] when it should have been ItemStack[9] 
  
So I've been out of the loop for a while and only mess around with Minecraft for java practice as I am a C# programmer, is this a MCP issue or actual Minecraft issue? or did I somehow get this isolated to me only?