Eating Golden apples and other food that give effects, there seems to be a random chance of the food being consumed twice, this only happens randomly I have noticed no pattern.

Testing I have done, this happens only if you keep the item you have eaten in your hand. Say you have 64 golden apples and you eat 1, and then quickly change to something else in your hot bar, it will not happen.

The items this happens with seems to be all food items that give the player a potion effect.