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Your understanding is correct. For a differential drive robot, the odom.twist.twist.linear.y = 0 as it is referred to the base_link frame. The other part of the Odometry message though will include X and Y position in the Odom frame.

See this page where the to different frames are called out. http://docs.ros.org/api/nav_msgs/html/msg/Odometry.html

As to why you are getting X and Y velocities, you'll have to provide some info on what your setup is.

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