For simplicity, I'll focus on just one detail of the book, that discredited it for me.
Figure 6.1 on page 115 (the lower panel) shows a rugged fitness landscape taken from Sergey Gavrilets (2004, "Fitness landscapes and the origin of species." Princeton University Press).
The whole book of Gavrilets is written, in order to prove this figure wrong. And it does so successfully. Behe, however, takes this figure as a proper illustration of a fitness landscape, as if it showed the current state of scientific knowledge about fitness landscapes.
Either, Behe took the figure without reading any smallest part of Gavrilets book. That would be negligence. Or he took it on purpose, knowing that it is an old, dated, and no longer valid illustration of fitness landscapes. That would be dishonesty.