Hey there-- I've had that problem too. But it only happened when the shoes were really new--as I wore them, and endured the pain to do so--they broke in and got softer. And yeah, I had to wear them with at least 2 bandaids each foot for padding. But it did get better and now I can wear them bandaid-less. But I do have scars. Its only been a few months so maybe they'll go away.
Have another really cute pair of Steve Madden slides with the thong thing that NEVER got comfortable, no matter how much I wore them--and I think its cause thethong part is too thin to really support the weight of the shoe--has a chunky heavy bottom--and so it cuts into foot to compensate.
A