I think all the manufacturers had some problems building engines that meet the EPA standards for diesels established around 2004. It really increased the complexity of injection controls and added pollution control devices. Most of Ford's issues were with FICMs, EGR Coolers, and the HPOP system to control the injectors.
The more complex a system is, the more likely it is to fail. As they managed to gather more data on failure points, they've been able to engineer better solutions.