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I fixed it by changing the stereoCalibrate flags. For example using: cv::CALIB_RATIONAL_MODEL + cv::CALIB_FIX_K3 + cv::CALIB_FIX_K4 + cv::CALIB_FIX_K5 + cv::CALIB_FIX_K6

Another thing that gave larger RMS error, but at least a correct remap was calibrating intrinsics and extrinsics together. So no cv::CALIB_USE_INTRINSIC_GUESS + cv::CALIB_FIX_INTRINSIC

For now there is nothing else I found to be working.