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short answer: you shouldn't combine octomap and gmapping like this.
long answer:
gmapping is a slam algorithm which goes back and re-optimizes previous poses based on new data, in order to do things like loop closure. This means that, during mapping, the estimated position of the robot may be wrong for a period of time, before gmapping collects enough data to correct the position of the robot. If you set the occupancy of an octomap based on these positions, you'll be building that position error into your octomap.
You should probably look for a different approach which incorporates the 3D map-building process into the SLAM algorithm.
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