When you apply a torque to one of the rod, it starts spinning around its axis. But since the rods have masses, the two other rods that are moving off-axis create inertia forces that eventually makes your system moving around all three axes. If you modify your system so that the joint is at the center of each rod, or add counter weights to make the make the inertia matrix diagonal at the joint, your will not have this problem anymore.
Also, you should also always add a World Frame to your model so that there is a common reference to define the position and orientation.
