The Bolt Connector in Simulation is a great way to simplify the study so physical bolts don’t need to be included in the analysis. In the case where you have a bolt going through the two holes, you only need to select the hole edge of the Bolt and the hole edge of the Nut on the opposite component.
However if you have more than two aligned holes (either more than two components, or a component with multiple aligned holes), you must enable the Bolt Series to indicate that the bolt also runs through the inner holes. Only select the hole faces of the inner holes. The two outmost holes have already been defined by selecting the Bolt/Nut hole edges.