I've loaded the WAA12SL exclusively for many many years, I don't count the wads but I do box as I load and there are always a few left in the bag after I've loaded a flat! Sounds as if someone at the retail end may be dipping in the bags before they sell them! I always buy them by the case and have never had a shortage problem! The last case I bought has the bags sealed which would make it more difficult to 'sticky' finger a few, however some years back the bags were closed with a twist tie!
I have had it go both ways, usually its +/- 5 wads per bag. There was a time when I went to great lengths to get my components to 'run out' at the same time. Now days there are lots of misc. little bags of wads,primers and spare shells laying around the shop. Life is too short to sweat the small stuff.