Any software patent can cause trouble for people who want to develop software.
Some software patents are Patent Office mistakes which cover things that are already known. Other software patents do not result from errors of the system, but are still disadvantageous to software development. How much trouble a software patent causes is independent of whether it violates the patent system's own rules. And the sheer number of software patents causes trouble regardless of their details. The SPI cannot prevent all patents which harm the software field.