I bet you colonized "red dot" worlds, having compatible planet type but incompatible atmosphere ...
These ones only have domed colonies, and space is restricted accordingly, but you should still have from 1 (tiny planet) to 15 (huge) spaces for facilities. Else you have a strange bug
Try to colonize "green dots" and large planets to have more room
(I've read that having a gas race can help here, as gas planets are fewer but larger).