Free ships, such as the 3 colony ships from Fairness or the Overlord ship from the nanite artifact, do not show up in my games since the previous update. Only the 3 mining ships from the tech research appear. This can be somewhat crippling for early games.
All the "free" ships are can only be received if they are the original version of that ship type.
If you have deleted one or more of those originals, you will not get free ships of that type.
You can design improved versions of these ships however do not delete the originals.
This is not a bug but works as designed.
Maybe it should be looked at as a future change, but only if they have the time as at this time there are many more important things to work on.
If this is not what is happening to you then post a save so the Devs can have a look.