لَمْ يَكُنْ مِنْ نِزَاعٍ فِي خِلَافَتِهِ
It was not due to a dispute over the legitimacy of his caliphate.
The pronoun in khilāfatihī refers to ʿAlī. The central claim is that these conflicts should not automatically be interpreted as a rejection of the legitimacy of his caliphate; they arose in connection with other practical judgments.
A leader’s rightful position and the best immediate policy are different questions. Parties may recognize a leader while disagreeing about how and when to respond to a crisis. This distinction frames the subsequent narrative.