With out a clear detailed facts ,it is difficult to provide a good answer.
Once the person representing the true owner was not genuine, it was always open to the Sub-Registrar not to return the document. A power of attorney can be granted by the party transferring the property (transferor) to the party to whom the property is to be transferred (transferee) for the purposes of granting authority to the transferee to execute the conveyance/sale deed in favour of the transferee, and registration of the sale deed on behalf of the transferor. Check the power of attorney is specific or general .
If specific power of attorney is issued it can only be used for acquiring property mentioned in said power of attorney.if general power of attorney is issued it can be used for acquiring another property provided power of attorney is registered