If it's leaking at screw holes, then chances are you misdrove the screw -- either it's in too tight and the gasket has broken (you *did* use the special gasketed screws for metal roofing, yes?) or it's not in tight enough so there is space around the gasket. You can visually check for either of those -- viewed from the side, the sides of the gasket should bulge out just a little, not be straight nor really 'puffed out'. If the screw is loose, tighten it; if it's too tight you should remove it, stick a toothpick in the hole in the wood, and drive in a replacement screw (the old gasket will never be the same again).
The only other possibility I know of, again assuming you used gasketed roofing screws, is - could you have accidentally 'doubled' those holes? I.e. started the hole one place, then moved over an eighth of an inch and did it again, so that there is a small 'leaker' hole in addition to what the screw goes thru. Even if it's covered by the gasket, those will leak. For those, I would put on a big ol' goober of exterior long-life caulk. It will look a little doofy if your roof is any color other than white, but better a blob of caulk than leakage
Good luck,
Pat
The only other possibility I know of, again assuming you used gasketed roofing screws, is - could you have accidentally 'doubled' those holes? I.e. started the hole one place, then moved over an eighth of an inch and did it again, so that there is a small 'leaker' hole in addition to what the screw goes thru. Even if it's covered by the gasket, those will leak. For those, I would put on a big ol' goober of exterior long-life caulk. It will look a little doofy if your roof is any color other than white, but better a blob of caulk than leakage

Good luck,
Pat