While trying to build my phantom for exploration, this situation just happened to me
And I was unable to swap my power plant out for a 5A version. It kept forcing me to "sell" my grade 4 6A pp, So naturally I would freak out and buy it back. I tried this a few times exiting the game and reloading menus and everything, I ended up trying a total of five times only to realize that each time I "bought back" my old pp, it was NOT REFUNDING MY 5A PP! The 5A would basically just evaporate. So every time this happened I was losing a little over 4 million credits!
I only had 100 million to start with so this has been a pretty substantial hit to my finances.
I eventually got it to work by reading someone said to swap another component from your storage. I did that with some thrusters I had sitting around and then I was able to properly store / swap core components as they should.
Just a heads up for anyone else who decides to do a lot of messing around with outfitting, If this bug happens to you don't just keep attempting it with expensive parts!