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You need to post your full EKF config and a sample of each sensor input, but the behaviour of the EKF is probably correct here: if you are just feeding wheel encoder velocities and IMU angular velocity, those measurements will be integrated, but so will their errors. If you want to constrain error, you need an absolute pose reference (input source).

However, the unbounded growth of the odom->base_link state estimate covariance should have zero bearing on the map->odom transform. Your jitter is going to be coming from another source. Please provide more detail in your question.