Most people seem to think Chris Eyre directs a film that follows the plot of A Thief of Time pretty faithfully on the whole (to many readers' satisfaction). A few, however, take exception to some of the changes. For example, in the novel Leaphorn has recently lost his wife, Emma; in the film, Emma is alive and a significant part of the story. This definitely changes Leaphorn's perspective, and influences the way he thinks about death (and especially death in Navajo culture) throughout the story. This deviation from the book is perhaps explained by the fact that A Thief of Time, the third film, is actually set before the second film in the PBS Hillerman series.
In condensing a complicated mystery into a ninety minute film, some scenes were lost and the story's complexity was reduced (as we might expect). More interestingly, several elements were added. Some were surprised by what they perceived as a different dynamic between Joe Leaphorn and Jim Chee, who, though they still have a relationship of mutual respect, appear less wary of each other and more unreserved in the friendship (Chee openly admires the older Leaphorn and, some think, takes less responsibility as a more innocent character).
Finally, some felt the film's ending was inconclusive compared to the book's, and pointed to the number of questions that linger about the motive behind the two murders at the film's conclusion.