How about in The Great Hunt when the Bastion is, what, 10k+ away from the Lucifer and command is hoping to have the Bastion close the distance. Really? I mean, command does eventually realize it's hopeless, but what was command's plan if it somehow did? Lob it to death? All the fighters/bombers already had the special subspace drives. Just launch ALL the fighters/bombers (ok, maybe save a few for defense).
I disagree with this, let me make my case real quick.
The Bastion could:
Provide cover, draw fire, and do some damage when it had the opportunity.
And Standard plasma/laser turrets are surprisingly deadly when shields are taken out of the equation, plus even a little Point defense is better then no point defense.
Not to mention Earth and possibly all of humanity's survival is at stake, if the Bastion can help even just a little bit it's worth it, heck, Kamikaze-ing the Lucifer with the Bastion would have been a perfectly legit plan in this scenario! This is an All-Costs mission!
Furthermore, The late arrival was due to the Lucifer being faster and more subspace agile, not to mention the Bastion was slowed by a surprise Demon attack in the mission prior.
Command makes some dumb choices yeah, but I think in this instance it's just bad circumstance.
Now a real bad case: Why did command tell the transport to dock with the shivan cargo after the first one blew up? Isn't shivan tech beyond most scanners at that point? Just because the scanners said it was safe does not mean it was! And the other one read as safe too, and it still blew up!
Command literally made the exact same mistake twice in a row and learned nothing.