Most likely you get this problem playing Fyron's Mod. Then you can get around it by starting games with "good HW value" instead of "normal". HW are now have "Large" sizes and can not be placed as moons.
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It is forbidden to kill; therefore all murderers are punished unless they kill in large numbers and to the sound of trumpets. - Voltaire
It happened to me once in a default game. That was a couple of patches back 'tho. I selected poor planet type and got a methane homeworld for an oxygen race.
I had more facilities than the domed planet could hold. Even so, I only had 3 research facilities.
The AI hosed me good in that game, couldn't find any breatheables within two systems.