Certified GKH Gardening Expert
Usually, this isn't a big deal. What is a bad thing is planting a tree in a container with mud. Clay is not a suitable media for container, as it tends to turn to mud. Once this dries, it will become like concrete which will starve the tree of nutrients and water.
This tree should be planted in a mix of potting soil and compost.
This article will help: https://www.gardeningknowhow.com/edible/fruits/pomegranate/pomegranate-in-a-pot.htm