Generally, painting popcorn is a terrible idea because it makes it much harder to remove, which is ultimately what should be done with it. And painted popcorn often cracks or otherwise looks even worse.
But you've already painted it, so re-painting it is unlikely to remove the popcorn...I would just re-roll it with ceiling paint. However I doubt you are going to get it looking good by only painting the spots, I think you will need to do the whole ceiling in that room if you want it ready to sell.
As for the suggestion to paint it with a sprayer or spray-can, I think you are going to end up with paint drifting onto your furniture or other parts of your house, so I would definitely not do that.