Yes.  CBT is an excellent and useful approach to therapy, but it has limitations, as all approaches to therapy have.
All approaches to psychotherapy are based on theories about human nature and the human mind that are useful but inherently limited.  Psychology and psychiatry have developed many theories to understand the human mind, and no theory has proven so useful and effective that it has crowded out the others and taken a dominant role in the field.
Regarding CBT, its theory emphasizes thinking and behavior as fundamental to human change and treats emotion as secondary.  I believe that this approach gives short shrift to the emotional side of human nature and is a weakness of the theory.  Focusing is a different, humanistic approach to psychotherapy that gives much more weight to emotions and the way we experience emotions in the body.  Focusing works to help the client gain awareness of a bodily felt sense, by holding an open, spacious, and nonjudgmental attention that helps the client clarify and understand his or her emotions.  Many clients have found Focusing to be profoundly helpful in ways that are quite different from CBT
CBT also operates in a very logical manner, which is both a strength and a weakness; the approach will appeal to some and will alienate others.
Another way we can look at the limitations of a particular theory is to consider what the theory leaves out.  CBT does not address the unconscious mind, i.e. the contents of the mind that we are not conscious of, nor does it address defense mechanisms like repression and denial, which are means by which we lose awareness of the painful contents of the mind, or the inner critic, the inner voice that criticizes and condemns us (the inner critic is usually very prominent in depression).  The unconscious mind, defense, mechanisms, and the inner critic (or superego) are all parts of the psychodynamic theory of the mind, dating back to the work of Freud and Jung.  I often find these concepts helpful in my work as a therapist.
CBT also does not address differences in personality type and development, which I consider a major limitation of the theory.  There are many approaches to psychotherapy that recognize the existence of qualitatively different personality types, and tailor their approach to the client based on which interventions are most effective with the client’s particular personality type.  Many theories also recognize differences in personality development or maturity, utilizing the rich knowledge of developmental psychology, which is important to take into account in working effectively with an individual client.  Psychodynamic psychotherapy takes into account both personality type and personality development, and the DSM-5 explicitly takes personality into account.  My favorite approach to working with personality is the Enneagram.  The Enneagram covers the whole range of human personality, from severe psychological disturbance to self-actualization, and also addresses the spiritual side of human nature in a way that is inclusive across spiritual traditions.  As a therapist, I find the Enneagram helps me understand my clients more quickly and more deeply, and helps my clients better understand themselves in a way that Cognitive-Behavioral Therapy does not.
To sum up, CBT is an excellent and useful approach to therapy, but it has limitations, as all approaches to therapy have.