But that's kind of the point of the article. Although there's no obvious flaw in the DFS code (it's not as if it writes out a list of files accessed in super_secret_files_are_here.txt) the whole idea of a Deniable FS relies on the applications and OS not giving the game away, and that's beyond the control of Truecrypt (or any other deniable filesystem program).
“Modern applications and operating systems are very complicated, and interact with each other in many different ways,” Schneier says. “Hiding the existence of something means controlling all those interactions, which turns out to be a very hard problem.”