They are (as LTjim is saying) most likely planets that require Advanced Colonization techs to colonize. If you by one way or another gain an Aquatic world, but don't have either of the two Aquatic colonizations techs, you will not generate any social or military production through factories. (You can recognise these worlds, because their icon will be red to indicate you don't have the techs, yellow indicates you have one of the two (production works at 50%), green indicates you have both techs. Research generation works as on any other world though, this also means that if you generate enough researchpoints on the planet, putting the Focus on social construction WILL allow you to build using a percentage (20% or 25%) of the researchpoints.  Buying works aswell.

If this is not the case with your planets, I wouldn't know what else'd explain it.