One fairly common side effect is severe muscular headaches / migranes as the stimulation stimulates muscles across the surface of the skull.

Another issue is potential complications with respect to seizures. I'm not sure precisely what percentage of people have TMS induced seizure with the procedure but some significant number of them do. There are issues around harm to the person in having a seizure (this is why people are sedated / restrained when undergoing ECT). There are also issues around the 'kindling' theory of epilepsy - which is basically the notion that the more seizures one has had the more seizures one is likely to have. As such, inducing seizures might result in epilepsy down the track.

As always there simply isn't a wonderful magical answer... Just the careful weighting of pros and cons...