Just as every job or institution falls short in some areas for potential candidates, it's also true for employers---simply because someone applies does not necessarily equal an interview. Everyone deserves a review. But some recruiters can feel it's their responsibility to give every applicant the benefit of an initial screening interview. Depending on the number of applicants, this can be a drain on employer resources.
As an employer, trust your screening materials. If an applicant falls short, it's appropriate to communicate that electronically, update your database, and move on.
Not every applicant must become a potential candidate.