At about 4:30 AM Pacific time, I was playing KA Space Normal and fought the tac cube in my tactical Odyssey on my tactical captain. The Aquarius was disabled at some point during that battle or shortly after it (possibly due to the tac cube's explosion as per usual). However, when I attempted to retrieve the ship it failed to work. The sound effects were audible and the 10 second countdown to docking fired off in the tray, but the animation never happened, the saucer sep remained greyed out, the button for the Aquarius did not switch to post-retrieval cooldown (and remained lit up as if waiting to be used), and for the rest of the mission I was stuck with an unusable escort (which remained disabled on the playing field) and no way to activate saucer sep.
I did use Work Bees on the escort, if I recall correctly, and it may have been a bit sluggish in engaging the enemy, but other than that I don't recall anything else out of the ordinary. I also don't think I did anything "wrong," either.