The only real question I have is have you actually seen the stones themselves? If not then the stones could give the dates in the book and the markers are wrong.
That's not to say there aren't plenty of errors in NIS, but it is at best a starting guide, and a good place to know where to start looking for stones to check yourself.
I've also heard that he was going blind in the later years of compiling NIS so that might have caused problems as well. I know the Maryland Room in the library has his original notes and records.