Sects and denominations naturally develop as believers come to disagree as to exactly what divine truth has been revealed to the faithful. Naturally each sect believes that all the others are either wrong or liars, though sometimes the differences between sects look trivial to outsiders. A denomination is like a sect but larger and more official, it's rather confusing.
Protestants and Roman Catholics have killed each other ostensibly because of differences over interpretation of what happens during the Eucharist. The real difference may have been over whether or not to accept the authority of the Pope. Sometimes religions split due to differences in doctrine. Also usually a major factor is who should rule.