This was brought up previously in
this thread started by Jeff back in April of this year. As mentioned in that thread, this has been going on for some time. It's hard to say if this is on purpose, or just a case of someone not knowing how to properly scan a card.
I have also seen this with Heritage, and again, I am not claiming that this is being done to deceive, as it might just be the result of a bad scanner.
Off the top of my head, some auction houses that get the scans "right" are REA, Love of the Game, Huggins & Scott, and Goodwin (although Goodwin's could be slightly more accurate). I'm sure other auction houses offer accurate scans as well. Ultimately, it's not easy to get a perfect representation of how a card looks in hand. Some scanners are great out of the box, others... not so much.
Here's a card from Heritage that shows the difference in one of their scans (the upper scan from the auction site, the lower one from my scanner, a Canon CanoScan 5600f). I was happy with the card, as I could tell by the flip that the contrast was jacked up, so I knew what to expect in terms of color.
When creases, wrinkles, dirt, smudges, etc. get covered up by high contrast, this becomes a problem.