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Unfortunately this is a known bug and it is being tracked in several places. I would recommend you open rqt_plot as a standalone app instead of opening it from within rqt itself. Then run new instances for each set of topics you would like to plot.
ros2 run rqt_plot rqt_plot
The underlying issue is that destroying subscriptions while a node is spinning in another thread is not thread-safe for python: https://github.com/ros2/rclpy/issues/255
RQT specific issue: https://github.com/ros-visualization/rqt/issues/181
There are possible workarounds for this issue in rqt, but to provide a stable API it was decided to wait for a fix to rclpy.
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