Sometimes it's a bullshit reason for rejection, sometimes there are real issues (these would be detected at various stages of the process):
poor communication skills
bitching about previous employers
having no idea about the company (or worse - mistaking it for another one)
some inappropriate remarks during interview (for instance sexist jokes or belittling various roles of people working with you, like QA or managers)
not having an appropriate level of interest in skills related to the job (as judged by the technical interviewers) - this varies wildly of course
so as you can see most of it is related to the interview itself.