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Octomap updates are pretty expensive CPU-wise, so you might be limited by that. You can check CPU consumption using the top command line utility. Also note that you should be using the Depth Image Occupancy Map Updater (not the PointCloud Occupany Map Updater) with RGBD-type cameras as it tends to provide better performance (see here).

Regarding the shape of the octomap it would be helpful if you could post/link a screenshot (by editing your question). It should be noted that RGBD-cameras generate fairly noisy data (esp. at longer ranges), so deviations from how the real world looks can be expected.