Not exactly a bug, but all factions should have at least one frigate with the "colonize" and and one with the "crew extractor" abilities or they won't be able to expand as effeciently or at all...

They do, you just have to look for it.

 

The CIS's is the Trafed Carrier, and some of the Cap. ships.

 

The Empire's is the Acclamator 1 I believe.

 

As for the rebals and republic, I haven't played them yet

You're correct about the colonization command, but there is no crew extractor function (used to takeover asteroids and such on non-colonizable worlds) on any ship in the mod.

Ah yes, I eventually found colonisers in all the fleets. It might not be entirely balanced that they're all different shiptypes. The crew extractor thing remains. It can be quite important on some maps.