Calame was guilty of confirmation bias; I believe he ignored a lot of contrary evidence on McCoy. Calame (or his FBI sources) claimed Cooper had McCoy's prominent ears. As far as I know, none of the witnesses put a pair of Dumbo-esque ears on Cooper. This is the most obvious "lie" in the book. I found a handful of other outright misrepresentations, but I'd have to go back through the book to find them.
I remember a few other, not lies, but examples of specious reasoning: Among them, they claim Cooper's hands weren't really nicotine stained, but that Cooper was wearing makeup (Like McCoy). And they said the airplane lighting prevented the Northwest crew from getting a good look at Cooper (to undermine the fact the 305 witnesses were probably unanimous in saying McCoy was not Cooper) even though the lighting was apparently enough to allow the witnesses to see the stained fingers).