I got a few similar ones, just less serious. If you refill the jump-thruster right before you land (and you are empty of fuel as you touch down). And then try to take off again, the tooltip with "refill the thruster with plutonium" flashes, and you can't launch. Or refill (again).
The Atlas quest also somehow will progress to the sanctuary meeting if you don't decide to spurn the red orb at the beginning. But if you don't enter and reject Atlas (you might not want to bother, if you've decided to go on your own way), the next "stage" of the quest doesn't trigger.
This is the same thing as the warp fuel blueprint. You're likely technically able to eventually get it from later "transmission" beacon missions, when you raid depots and so on. But unless they've made sure that the first blueprint you get is the warp-core, then good luck with random production blueprints..
The Photon-cannon also seems to have been rechargeable in an earlier version. So now if you "empty" it, it stays empty, and can't be refilled. Best guess: something was changed with the starter ship in a forced script to make it easier to play, and the scripts or functions carry over. And no one tested that.
So two logical scripting bugs (that should be visible to anyone who tests the game - break "complete" condition and leave, see if the mission respawns...), and leftovers from (presumably) some professional grade "streamlining".
I want to say "I wonder what they were doing during the delay", but I guess it's pretty obvious..