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Costmap transforms measurements into the maps frame, so it does, what it's supposed to do. If you think about, what is happening, transforming the obstacle messages relative to the robot's z might solve the issue. But essentially I think you are in case 3) You have costmap_2d and put a 3d problem in that. That can't work in general. You can transform your 3d problem back to 2d or 2.5d, but that requires understanding, what you want in the 2d formulation from a 3d world.