Have you marked core ship designs as obsolete? The anomalies are set to give you ships which are of designs from the base game, and there used to be an issue where marking core designs as obsolete would screw with the things that provided free ships (e.g. if you marked the standard Constructor obsolete and then picked the Pragmatic trait that gives you three Constructors, you wouldn't get any). This was supposed to be fixed by patch 1.01, but I don't think that the patches affect games created before the patch was applied.

Please update and let us know if this was fixed in 1.02 for you. If the game was started with 1.0 or earlier we would absolutely expect the issue exactly as you described.

It should have been fixed if the game was started with 1.01 or later. So if you are seeing it with 1.02 please let us know and let us know what faction you are playing as (if you are playing as a custom faction please let us know what ship style you are using).