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holes in shell

* Abrasions: your turtle might be rubbing itself agains some 
  rocks in the cage. Remove the rocks and it should heal.
* Poor shedding. If your turtle does not shed scutes well, water
  collects under partially shed scutes; a paradise for bacteria.
* Bites by another turtle.
* Husbandry issues, leading to shell rot.
* Somebody actually drilled a hole into the shell
* dog bite