I'm scraping all the paint off the body atm and getting to do my first full size paint job, there was some small bubbling of the paint that was identical to the rust spots underneath but as I scraped I also found some of the same rust spots under the paint where there was no bubbling at all. Same extent of rust, same thickness of paint over top, just thought that was strange.

So is this the result of too much time between sanding and spraying primmer?
It is pretty thin rust, 5 secs of 60 grit with an DA sander and it's gone but wondering if I should go deeper just in case?
Thanks.

you need to get ALL the brown off, then try to get primer on it a soon as possible. 2 coats of epoxy and your good to do anything you want at any time. you'll need to scuff it for bondo if you let it go out of its sensitive state.
Jay D.

You can sandblast those areas and they will clean up real nice.

im not the smartest on all this, but it seems that if you found rust under the paint while scraping the rust could have started on the backside and what you see on the exterior could be just a small part of the rust problem. i hope im wrong,though.

Tom your very right rust from the back side is very common. In the picture it looks like surface rust. but if the O/P has access to a sand blaster that's the way to go and usually if the rust is from the back side you'll end up with a hole or holes.
Jay D.