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After talking to Bill Morris from iheartrobotics, I changed my setup a bit. He suggested that it may be a problem with node priorities or nodelet managers miscommunicating since I had roscore running on a different computer than the TurtleBot. Instead of having a master node that runs ROS, I made it so the TurtleBot laptop was running ROS itself. With that, it has consistently run without the costmap errors. For the most part it runs smoother with commands. Now rviz and viewing the map in real time is slow, but that's alright.