Duplicating items in inventory / fishing rods in inventory auto repair

When I go to feed/breed the cows if I have a total of 6 wheat in my inventory, after I feed two to the cows and stop, not all the time but sometimes when I open my inventory I will have two stacks of 4 wheat instead of just 1, another issue I am having is earlier today I was fishing, I had 2 enchanted rods in my inventory and when I went to fish I had fished up a new enchanted rod for a total of 3 enchanted rods, when I went to put the rods back in the chest I only had 2 enchanted rods but the durability on my most worn down rod had gone back up to nearly full durability, so I don't know how this is happening but it is kind of annoying