Body help/advice needed

Did some sanding the last 2 nights. On the trunk area I found some dark spots in the metal once the paint and primer was removed. Not sure if I should be concerned with this. Let me know what you think. I am attaching a few pics

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As you can see they are dark spots but I cant feel them as I slide my finger over them. Was wondering if I should treat them with a rust inhibitor before i shoot primer. They do not sand out.

Thanks
Rod

I use a product called Ospho to treat rust spots.