I actually did obsolete some ships. Maybe the constructor ships I obsolete resulted in the technology not being able to reference any ship and resulted in 2 blank ships. That could be it.
Never obsolete the original Civilian ships.
Colony, probe, constructor, asteroid miner, supply ship, or any you can get free versions by event
You will not get the ones from events/techs or the ones from using control pts like buying free colony ships.
This is not a bug might be considered poor design but is by design ATM.