Any chance someone backed into your bumper while it was parked? That might explain the fender being set back a little. Otherwise, that is pretty unusual.
I had the same on the driver side. But the fender was probably 1/4" higher than the hood. Body shop here said that was probably the worst from factory they seen... They fixed the fender placement and patched up the door with some touch up paint.
Easy fix. Just unbolt the quarter panel and shift it forward. I've done minor adjustments to all alumimium panels/bumper covers on both of my GT350s. All you need is a 10mm socket and some touch-up paint applied to the bolts after they're torqued back down.
To cover some of the comments. The car didn't appear to have been hit in any way. The only measurable difference I could see was that it was a hot day in full sun.
Don't have pix post adjustments, but it was not easy to get clearance without mis-aligning some of the "lines". I managed to get about 1.5mm of clearance after adjusting it.
There are 3 10mm nuts on the flat side of the fender under the hood. Then there are 2 8mm nuts in the areas I highlighted in the picture. This was enough to give me some wiggle room to adjust (There are additional bolts on the lower part of the fender but did not need to loosen). Make sure you bring the hood down slowly and correct the hood gap before final tightening.