I really think this type of thing confirms that it might be wise for the major clay court tournaments to invest in hawk-eye in the future. Looking for the mark is fine in obvious situations, but in situations like this it's just not sufficient.
Hawkeye is still significantly (statistically speaking) less accurate on clay (an uneven surface that is constantly being slid on, dug into, and swept, all of which complicate the technology). Given the technological limitations at the moment, looking at a ball mark up close with your own eyes remains more reliable. Even in the Sharapova/Kvitova match, there is still reason to believe that Hawkeye's projection of the shot was off enough that the ball was
out. (See also: Wozniacki, "Did you go to school?")
Who knows? It's not 99% reliable like on hard courts or grass. If the ball lands in a small divot left by a player's slide, for example, then Hawkeye's triangulation would certainly be affected, even slightly, which is all it takes to screw up a close call that might be clear given the ball mark.
Can you imagine a scenario where a player challenges a call on clay and Hawkeye calls it IN, meanwhile the TV camera clearly zooms in on a obviously OUT ball mark visible with the naked eye. Incidents like that would destroy all trust in the challenge system on all
surfaces and players would be irate.