Weird orange rust spots appearing in holes on freshly painted basement cinder blocks
The orange stain is likely an iron ochre infiltration due to high levels of iron in the soil or pre-existing iron in the cinder block. More info

The paint is simply making the orange much more visible than it was on bare cinder block.

I highly advise reading this article on basement finishing before continuing to paint your basement. You will likely have to re-paint next year because moisture is merciless and you might even cause mold issues for yourself which weren't present before.

If you really want to make the cinder block look nicer then you can try staining it. More info

Below is a picture of my basement wall which was Drylok'd about 4 years ago by the previous owner. Note: it looked like new when we moved in and it quickly went to crap.