Hi,
A RC filter is formed by just a resistor and a capacitor. It removes the higher frecuencies while leaving the bass ones to pass: maybe it will help in your case, but I'm pretty much sure it's not going to solve it completely (there will remain several shoots every pass).
As I understand the (laser?) light passing trough the notch hits a sensor that generates the electrical impulse. OK: try liming (polish) the edges of the notch as the laser could refract on them and generate "secondary" beams (maybe painting the CD black will help too; I know that this maybe incompatible with your project but, by the moment, I would concentrate on solving the interrupt multitriggering problem).
If the problem persists you have to ask for somebody to analize the output of the sensor with an oscilloscope.
The good new is that the output circuit (form the sensor to the arduino) is (or, at least, could be) electrically isolated from the CD motor circuit, for it is optilcally coupled.
Regards.