I have had good luck using snap traps and peanut butter. Especially if they dig there again.
Did you recently add any fertilizer or top dress that area?
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Bunny or a squirrel probably bit it in half and left it. They do that in my mom’s yard with stuff. Bit a gooseberry I planted to 3 inches tall … Then it grew like crazy 
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I did not add any fertilizer but dug the hole to plant the tree this spring. I then added shredded mulch after planting and when I mow the grass clipping tend to build a bit on top of the mulch. I’ll try collapsing the hole and will see if something digs again. So far, I have seen a groundhog, a snake, chipmunks, squirrels, and rabbits this season while mowing so I’m guessing it could have been a fair number of things creating the hole (though I’m sure rats are also around and I can hear frogs/toads at night).
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I’m glad it grew like crazy for you! I have a feeling that the seedlings won’t be able to come back but I’m coming up with plans for how to protect them the next time around. The funny thing is that I had transplanted a few seedlings from one pot to a mulched spot in the backyard and those transplanted ones have not been attacked.
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