"Using Magnets" is a little vague! What will they be used for? If it's to provide energy to propel the vehicle somehow, the answer is no. There may be many allowable usea, if we knew what the rules are.
The general idea is that all energy to propel the vehicle must be stored in the mousetrap. Once the mousetrap has been released to start a run, energy may be transferred from the mousetrap to other storage devices. Those other devices must have no usable energy (to propel the vehicle) except that which is transferred from the mousetrap.
Energy transfers are seldom used because they are never 100% efficient. Energy is lost with each transfer, leaving less available to propel the vehicle.
Information expressed here is solely the opinion of the author. Any similarity to that of the management or any official instrument is purely coincidental! Doing Science Olympiad since 1987!