I've had airline machines fail to scan the barcode on my poorly printed paper boarding passes (e.g. faded ink or unfortunate located gaps etc in the barcode area). The solution is simple, just type in the details off the BP into the terminal to look up my PNR and type the command to confirm I've boarded. I've seen this done for both paper and mobile boarding pass issues. Not a mobile issue but obviously poor staff training and problem solving which occurs with or without mobiles.