Bought my 2017 GT350 new back in June 2017. Just last week I noticed some spots of rust developing in the jamb of the trunk. At first I thought it must've been something else, but after rinsing the area with soap and water and wiping it clean, I'm 100% sure it's rust.

Fewer than 9000 miles, it's kept in a garage in Southern California and hardly ever driven in the rain.

I'm wondering if anyone else has noticed this...

I'll try to attach pictures.

 

Have you tried to clay bar it? It could be tree sap. If it comes off (sap) then make sure you wax the are to reduce it getting stuck there again?

 

Try to clay bar it. It’s probably what does calls environmental fall out.

 

I suspect you have a unique problem with your car here. It appears to me that it had some grinding debris on the bare sheet metal when it was painted. In other words the paint prep was poor on this particular car. You might have a warranty claim here with Ford.