In Navisworks, the sectioning tools have two different modes: section planes and section box. The BCF Manager only supports Navisworks section planes. That means, if the section is created by the section box in Navisworks, it will not be saved in the viewpoint when creating issues in the BCF manager.
📝 Note:
To easily create a section box using planes, use the 'section box' tool integrated in the BCF manager.