Any idea how I can resolve this these two rust spots

Are you near Lansing? You might check with Keith Armstrong.

 

I assume you want to do this DIY?

If you're finicky about paint, you're not going to like how this goes. First off, remove the black cover in the second photo. It looks like there's more rust under there. You need to scrape off the bubbles with a scraper, sand the rust off, etch the metal, and seal it. Then cover with touch up paint that matches the body color. It's not going to be perfect, but it will look decent, will protect the metal and keep the rust from spreading.
I recommend the POR-15 Starter Kit.
If you want it to be perfect, take it to a body shop and they'll do a professional job. You'll pay for it, but you'll not be able to tell that it was ever there.
Personally, I'd DIY it. But that's just me.

Good luck!

 

Unfortunately that appears to be coming from beneath rather than a break in the paint surface. Probably more will follow in time.

Since this is not exclusive to the Prius, I suggest you review Utube. With moderate you'll keep it looking good.

 

Grinding, sending, rust proofing, filling, sanding, prime-ing, painting

 

With an 8 year old car that has 103K miles.....that kind of goes with the territory and trying to "fix" it might be a mistake.
The little brown spots on the flat panel probably just need to be kept polished and waxed.

The ones showing signs of "bubbling" could be scraped a little and some touch up paint added.
Personally I think that would be a waste of time.

 

Agreed. My daughters 2008 has never been washed or waxed,, yet looks like new, albeit a bit grimy at times. Maybe it protects the paint