What kind of soil did you put in those pots? Garden soil? Chickens will never hurt plants. They eat bugs, seed, tender baby plants like weeds...they do not dig without a reason or a motivation.
Your potted plants look like bamboo? The rocks were a good idea but the chickens were after BUGS in the soil that shouldn't have been in the soil of your pots. Potting soil is sterilized, very little soil actually, but perfect medium to use for potted plants.
Garden soil in pots will not have the benefit of the larger body of soil in your garden that also houses beneficial organisms that keep other insects/disease in check. Your chickens were after insects that should not be in the soil of your potted plants.
So cute. I love chickens! The best 'coops' are the ones that you are able to move around the yard allowing your chickens to eat weed seeds and insects to their delight. Always caged. It is safer than allowing them out during the day with no supervision.
Those pots have some yummy insect in the soil. Chickens are doing you a favor.
Have you fertilized the plants in the pots? What soil is in the pots?