Was there any disagreement among the people about what to do when Sai Baba was in his three-day samadhi?

Yes, there was significant disagreement and concern. Chapter 44 describes how after two days passed with Baba showing no signs of life, some people, including Maulvis, Mullas, Fakirs, Appa Kulkarni, and Kashiram, concluded he had passed away. They made a firm decision to "give rest to the body." However, others strongly disagreed, arguing that "such haste is not good" and that Baba's word was infallible. This group insisted they wait, as Baba had said he would be in samadhi for three days, leading to a deep debate among the gathered crowd about the right course of action.