I'd chalk most of it up to user incompetence. Of course Harmon/JBL/infinity makes a shitload of gear so law of averages say they would have a good ammount of factory defectives too.
I bought one of the refurbs for a friend's car and I though it was a great amp for the money and we didn't have any reliability issues with it. All in all, I've had good luck with all te Harmon/JBL/INFINITY products I've used ever and I've used quite a few. IMO same quality or better than most of the really big brands (Kenwood, Alpine, RF, Pioneer, etc.) and generally a better price.
We are talking about the company that made the GTi subwoofers and the Crown amps... They have low mid and high end offerings and all IMO are pretty competitive in their classes.