Since the second (SFO-FRA) flight has a line item "Executive Bonus", that confirms that the second flight could not be allocated properly a revenue value and reverted to mileage based earnings. I presume this has to do with the mixed class nature of the booking?
Almost 13K miles is also way too much for FRA-LIN however you try to cut it, so it seems to me that it happenned that all of the revenue was somehow assigned to the connector leg within Europe. Which in practice means you ended up with 2x the miles.