Tool disappears at random when feeding animals

I built a house, I'm growing pumpkins and wheat and I created pens for chickens and sheep. Whenever I feed the chicken some seed or I feed the sheep some hay, one of my tools disappear. First it was my enchanted shovel, then my enchanted sword, then my enchanted bow. After the third time a tool disappeared I stopped playing this world but I'm hesitant to create a new one in case this happens again. It this a known issue? Thanks.