There are certainly problems with Behe's original definition. For instance the "well matched" criterion is an error. The whole idea that biochemistry can be broken down to well-defined systems with strict boundaries and a single well-defined function is also open to question. Behe was even unclear on what constituted a component - leading many readers to think that he meant that each protein in the flagellum should be considered a component.
But the biggest problem is in dealing with what Behe calls "indirect" routes of evolution. Behe was badly wrong to dismiss them in a single sentence and many people have wrongly believed that Behe ignored them altogether (on one side criticising Behe for the omission and on the other assuming that such routes could not exist - as Dembski did). I would argue that we should EXPECT evolution to operate by indirect routes and what Behe considers unlikely is in fact normal.
I would say that Behe's idea that the indirect routes are unlikely is also the result of thinking about evolution in the wrong way. The specific route may be unlikely. The actual system we see may also be unlikely. But that evolution would follow indirect routes and produce IC systems is - IMHO - not unlikely at all, in fact I believe that it would be very unlikely that we would not find IC systems.