I take the utmost care with storage (upright, not overloaded, etc.) and only use the best products. It's not a widespread problem I have, merely a few cards in a few different sets. The cards that are affected, they were never replicated, so perhaps the finish on the card is the issue. Even all my Finest and Chrome cards (notorious for curling) remain flat and in perfect condition.
This image shows 3 cards from 1998-99 Fleer Brilliants. These cards have spent their entire life in penny sleeves, brand new ultra pro pages and upright in a folder stored in a cupboard with 29 other folders that do not have this problem. The real damage is hard to see but the clear film on the cards has blistered and lifted away (the foggy lines and patches across the body), you can see the gold foil is missing in some parts on Wallace and is spotted on the 'Zo card in the middle. Camby is an example of how the card should look. These cards have a highly reflective, mirrored finish (nothing like a hologram).
On the other cards, you can see black spots over the gold foil on Francis and the section in which the player's name is printed on the Reserves was and is still meant to be an intense glossy red that stands out from the gold finish over the entire card, it has since faded to a yellow colour. These are the only sets amongst hundreds that I have that are showing signs of delapidation.
Maybe it's just these sets?