Natalie Scott said Miles attended the rehearsal on Saturday in Los Angeles but the family was told Sunday morning he would not be part of the ceremony.
"I don't know if they ran out of time, of if there was something about the segment they didn't like," Natalie Scott said. "It got pulled so quickly that we didn't have a lot of insight into what was going on."
Scott said the family hasn't been told why the segment was dropped.
Scott told IBF that Miles has completed his treatment for leukemia and is doing well.
The city of San Francisco turned out by the thousands in November as Miles, dressed as Batkid, battled villains around the city. Even President Barack Obama sent Miles his best wishes.