I seriously doubt if the wear on the shorts is from the saddle, although it cannot be ruled out completely.
One of the things that is deadly with lycra, as I have found, is velcro. And indeed, I have one pair of shorts with a worn spot on the inner thigh where the material would catch on a tiny flap of velcro with the hooks that retains the front of a stoker's bag on the tandem.
I've also had shorts catch on a sharper-than-should-be corner of a seatpost, this when I first fitted my Brooks Ti Swallow. I wrapped the offending part of the seatpost with some electical insulation tape.
On further occasions, I have had rub against the seatpost collar, although there was no damage there.
Have a look and feel around that area of your bike and see if there is anything that could be the culprit.
If Bike Fixation coughs up a new pair of knickers when there is unlikely to be a defect in the material, that would be ranked as truly superb customer service.