It might be the reason, but I see a problem here as well - I have to invent all the research levels for the subjugated colonies again , once using the Starting Facilities as 'Default'. I would be interesting how the game AI reacts after a conquest of more developed system...I just checked and all empires are at TL7 except the Cardassians which are at TL6.
Maybe those colonies were somewhat recent? They probably focused on building Buildings (especially resource production) before upgrading PFs beyond levels 2~3.
Edit: I have checked that above and it looks OK - I have access to construction upgrade of next levels.