Assuming you are using transistor H-bridges, place opposing diodes across the CE points of your H-Bridge drivers. This will greatly reduce the voltage spikes from the motors. See example at: http://www.robotroom.com/BipolarHBridge.html
It is unlikely that large spikes are reaching all the way back to the Li battery terminals, but spikes could cause uncontrolled behavior of rest of your circuit. A voltage spike into the reference pin of a voltage regulator could cause a temporary unregulated condition (a higher or lower output).