Hi
Than I think you should raise an OSS note to SAP because this is strange behavior. I faced an issue at the time of PGI that system created two material and accounting documents for one delivery and stock was issued twice. I searched and found an SAP note stating that this is due to unknown technical error and they gave a program to adjust the stock. In your case may be they would be able to give you a similar program or you can search in SAP service market place for some existing note.
In my opinion this is not normal behavior and there must be some technical issue with this. I believe you are facing this issue first time and for only one document. Is it so?
Thank$