I don't think it's especially controversial, as sources go. There are a number of tricky issues, but that just comes with the territory when you're analyzing primary sources. Gray's "Confessions" is just about the only source we have for understanding what Nat Turner was thinking. However, like all sources, it comes with a collection of caveats. The Confessions of Nat Turner was not written by Turner, exactly. Gray served as Turner's amanuensis, interviewing him over the course of three days, writing down what he said, cross-examining him, and then structuring the narrative as he saw fit.

So the first question is, who was Gray and why was he doing this? Gray was a lawyer, but he was broke, so his main interest was probably to make money with the publication of Turner's Confessions (which he was successful at). He was also, like most whites, deeply disturbed by Turner's recent actions and wanted the public to know what Turner was about for their own education and future safety. Learning why Turner did this could help prevent future slave rebellions. Gray clearly does not like Turner, and throughout the narrative interjects biased language in this vein. It's likely that Gray added his own phrases to the confession to make it more dramatic and give it more punch. Gray was also convinced that Turner was insane (because why else would a slave rebel?), and structured the narrative to give this impression.

At the same time, Turner's voice can be heard in the narrative too. So now the question is, why was Turner talking to Gray (whom he hated), and how honest was he? There is certain information which Gray would have no reason to alter or fabricate. Turner probably had reason to be honest, because he wanted the public to know why he had taken these actions, and Gray was the only game in town. Nevertheless, there are many issues which Turner remained silent about, for reasons which he took to the grave. It is not an autobiography, and Turner does not talk about major factors in his personal life--his wife, his relationship with his masters, or his personal experiences in slavery. He also does not say what his ultimate intentions were with his rebellion.

Probably the biggest problem is that Gray claims that he read the finished Narrative to Turner at the trial, and Turner said it was accurate. This is a lie, since we have the trial records. So we don't know what Turner would have thought about the finished product.

The version of the Confessions edited by Kenneth S. Greenberg, published by Bedford/St. Martin's, does a very good job of contextualization. Another very good analysis of Gray and his efforts is "The Construction of The Confessions of Nat Turner" by David F. Allmendinger, Jr., in Greenberg, ed., Nat Turner: A Slave Rebellion in History and Memory (2003).