Might be something or could be working as intended. Playing on a Small map with 3 other races.

I was at war with the Yor and needed to quick build a custom built ship, as a Yor transport was heading my way. I used the Build Now option and paid about 3000bc for the new class ship. The very next turn the Yor invaded my planet, As I looked at the newly Yor planet there was my ship but it was now a Yor ship..

With my all my resources used up on my last ditch effort to bring the fight back to the Yor. The new ship quickly tore into my already sub-standard forces and lead to the defeat of my empire.

Pretty lame, I thought but atleast it was a rare occasion.