This can be common squirrel behavior and there are no easy answers. They like digging in loose potting soil and there are no easy answers. Try laying some pine cones or sprinkling crushed oyster shells over the soil surface making it inhospitable for them to dig.
You may want to try covering your plants with floating row cover to exclude them. http://extension.umd.edu/growit/beyond-basics/floating-row-cover
If you feed the birds, you can also experiment with not feeding them for a period of time. Bird seed is a food source for squirrels.