If it is rust, it'll be covered by warranty. Strong possibility that it isn't rust, though. It could be tree sap, road tar, or something like that. I thought the paint on my Lexus was rusting too, all I had to do was clay bar the area to clean off the debris, then I polished the area and applied a layer of wax. Good as new, and the "rust" never came back.
It is rust, there is no paint on those chips and paint is bubbling around it. Today I took my CX-9 to a body shop and they confirmed it was caused long before I purchased the unit. Since it is a 2017 unit, I think it was stored a long time without supervision and who knows what conditions or what really happened in that time. After visiting the body shop I drove directly to the dealer and demanded to talk to the manager. Talked to him and tomorrow they are going to investigate the issue directly including other not resolved issues. Right now I'm starting to regret my decision to buy this unit.
Including the rust this is my list of issues so far:
1. Infotainment screen (replaced because of condensations and humidity inside the screen)
2. Exterior black piano trims pillars stained and scratched by the dealer (replacements were ordered by the dealer, waiting for parts)
3. Right tweeter (Bose) not working (replacement ordered by the dealer, speaker was defective, waiting for the speaker)
4. Driver side mirror shakes like hell after 65mph, it is unusable after this speed (dealer needs to investigate the unit further)
5. Headlamps shake in all roads condition (dealer needs to investigate the unit further)
6. The instrument cluster was disassembled to remove visible and annoying dead bugs under the LCD. Now is all swirled and marked by the technician who removed it.
All of these in my first month of ownership, I exhausted.