That's mysterious. Really no way to know if it was the squirrels or someone else who took them unless you set up a webcam. Were there tooth marks in any of the potatoes you found? I can't see a squirrel transporting dozens of potatoes that distance before they discovered they didn't want to eat them. More likely a larger animal. Watch for tracks in the soil and droppings?
Suggest you could spread chicken wire on top of the soil between the plants to prevent this happening in future. Just roll it up when you want to harvest, then lay it down again, weighted with bricks or rocks to keep it in place. You might still lose a few potatoes but if you make it difficult enough, whoever is doing this will eventually give up and go elsewhere.
