If mother rats have a particularly hard time birthing, there can be losses in appendages while she has to assit herself in pulling them out. Or sometimes new mothers will be cleaning up the newborns and nibble away a foot here, arm there. It would look completely healed over in a few days, and as they grow you wouldn't notice anything much like you have with yours.
The ears I can't explain. Thats just something I would have kept to play with.
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