How did you make diplomatic contact with them, in order to make any deals with them. Also how far into to the game, i.e. number of turns and amount of exploration done by you, were you?

Maybe the governors had low loyalty and because of that they defected to you.

I once got a core world from the Altarians. The governor had low loyalty. At least I think he defected. I got no message saying what had happened.

Well, I didn't get any notice either.  So that could be it.  One (the first) now has a loyalty of around 50 (to me I guess) and the other is green so it is at least 79.  And I cannot gift them a Harmony crystal for 100 turns.  I didn't get any message either.  Maybe the real issue is that there is no message concerning a defection like this.  It is not like the situation where you take over the planet by influence.  It is just out of the blue.

I have found another possibility for the planets to flip.

I'm alone in my sector.  When I was able to go into the next sector, I met the Corporate Sector.  Later, I don't know how long it took, 3 of their planets flipped to me in just a few turns.  Two were core worlds that became colonies, and one was a core world that stayed a core world.  I didn't see any notification and wondered what was going on as I had already seen this post.  The governor of the planet that stayed a core world has a loyalty to me of 70.  That planet also is 37% in rebellion due to influence, so it's going to be interesting to see what happens.

Later, I realized I had send a diplomat to them.  When I checked the diplomat, I found this.

That is probably the reason these planets flipped to me.

I found another candidate with that attribute, so I hired him and sent him to be a diplomat with another race.  It has been just a few turns, so it may not be enough time for any planets to flip.  I may have try this more often.  I also may have to be very careful if the AI decides to try this on me.

Well, my Minot diplomat had the "Make assigned race's planets more likely to defect to you" trait.  So, if this is the cause of it, it may be a little too powerful.  I'll try it on my new 0.65 game if it gets that far.