We study the interplay between motor programs and their timing in the brain by using precise pulses of transcranial magnetic stimulation (TMS) applied to the primary motor cortex. The movement of the finger performing a tapping task is periodically perturbed in synchronization with a metronome. TMS perturbation can profoundly affect both the finger trajectory and its kinematics, but the tapping accuracy itself is surprisingly not affected. The motion of the finger during the TMS perturbation can be categorized into two abnormal behaviors that subjects were unaware of: a doubling of the frequency of the tap and a stalling of the finger for half the period. More stalls occurred as the tapping frequency increased. In addition, an enhancement of the velocity of the finger on its way up was observed. We conclude that the timing process involved in controlling the tapping movement is separate from the motor processes in charge of execution of the motor commands. We speculate that the TMS is causing a release of the motor plan ahead of time into activation mode. The observed doubles and stalls are then the result of an indirect interaction in the brain, making use of an existing motor plan to correct the preactivation and obtain the temporal goal of keeping the beat.