I don't often see the squirrels digging UP anything I planted.
What I do see is signs of squirrels BURYING their cache of tree seeds "for later" -- especially late summer through fall. Sometimes, in the process, they disturb where I might have sown seeds or little seedlings are growing. Occasionally, but not often, this happens in flower pots and window boxes.
They usually bury using same technique as I use when planting garlic cloves and flower bulbs -- while pulling open the hole, push the object into the bottom, then let the soil fall back in over the object. So most of the time, it's just a single squirrel front paws sized hole about 1" in diameter and a little bit more comet streak scratch and pile of potting mix.
In spring through early summer, they sometimes remember that they buried something and (try to) dig them up. Often, by that time, I've been planting in the container or garden bed, and had unearthed their treasures and tossed them over by the back fence.
They do seem to make bigger messes then because they frantically *search* the spot and dig in several directions.
Most of the time, I discover they had planted their snacks because those seeds sprout and grow "volunteers" -- a lot of hickory, oak, and plum (they eat the fruit and bury the stones)... Maybe some of the cherries as well.
They seem to be just as busy burying them in the middle of the lawn as in garden beds.