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Looks quiet similar to this question. You probably have at least two different nodes publishing a tf transforms to the same parent frame.

In order to work properly, each transform can only have a single parent and needs to be connected to the other (related) transforms in a tree like manner (e.g. [map]->[odom]->[base_link])

If i understand you correctly you are using a single instance of robot_localization that fuses only local information (e.g. odometry, IMU) with respect to the [odom] frame. According to your description your gazebo plugin publishing an additional [map]->[base_link] transform. You might want to disable this tf publisher or use a separate frame name for the ground truth reference.

If you need further assistance please provide more detailed information of what you are tying to achieve and the relevant parts of your robot_localization configuration.