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  1. Is this error something bad and I should worry?

Maybe. Apparently there is an error in the management of ShapeHandles somewhere in the interaction between planning_scene_monitor, point_containment_filter, and pointcloud_octomap_update Feel free to investigate. It might be that this is a cleanup problem that does not notably affect normal operation.

  1. Can I resize the size of the hole (or box or w/e) that is done in the octomap?

Yes. This corresponds to the padding_offset parameter here: http://docs.ros.org/kinetic/api/moveit_tutorials/html/doc/pr2_tutorials/planning/src/doc/perception_configuration.html