Were nails or screws used? If it was nails, then sealing them wont do anything because the nails are loose and the metal will continue to move on you.
Either way, make sure your fasteners are tight. Screws might have to be replaced with longer ones, and nails should be replaced with screws. Tighten them so the rubber gaskets just beging to bulge. Do not overtighten them, because the rubber gasket can break or turn on you, which will then leak.
There are quite a few pretty good products out there for sealing holes in a roof. Henry is sold at Home Depot, and a product that I've had really good results with. There are others, but I've found that you get what you pay for is sealers. The cheap stuff isn't worth the savings, especially when you have to go back up there and remove it to put down the better stuff.
Read the labels, buy a sealant that is rated for flashing and/or metal. There are a variety of sealants out there, but not all are for use on metal.
Good luck,
Eddie