Orzelek; correct, building a colony ship from a shard requires the refugee outpost (and a home command station, for that matter). I'm guessing you just ran afoul of that particular requirement
In general the progression is not tolerant of failure, currently because it would take significantly more time to put in failure and recovery branches for everything but also because thematically it doesn't fit for most of the step.
That said, it shouldn't absolutely require the outpost once you have a city, so I can look at changing that, thanks for bringing it up.
On another note, I realized one reason you're catching it a bit harder than most of the testers: it wasn't scaling the chase-spawn-intervals by combat style. I'm talking about the ships spawned to chase a shard or the refugee ship during a recovery mission. Since you were playing on Epic you were catching 2x as many of those spawns even if you immediately gave the shard a move-to-homeworld order. In my working copy I'm having it use 2x the interval for Epic and 1/2x for Blitz.
At some point will also look at applying a more moderate scaling for the time between the city-hub-provoked event-attacks; that wouldn't be 2x, but maybe 1.2x for Epic since it does make it take longer to take planets, defeat attacks, etc.