Not sure. But I found this happened when I got the free ships that spawn after using Culture points and also when I found ships after studying an anomaly.
I have a custom civilization but had the same thing happen when using the humans.
Thought they fixed this months ago.
Remember asking on one of the forums and being told it was.
Could 2.94 have deleted that change?
Have never deleted my Originals anyway and do not get this but do delete my Original probes and asteroid miner as I have buffed their speed or range