Did you use the Leave System/Abort option on the HUD, or Leave System option that pops up after the STF was over? That will make a difference. Sometimes the Pop-Up doesn't show for 30-60 seconds after an STF is over, and that does make a difference. Dumb I know, but a bug that most likely will never get fixed any time soon.
so if the popup doesn't show and you just wait for the timer to track down will that avoid the issue? because tbh I haven't been patient enough to wait sometimes when the regular message completion pop up doesn't show after a few minutes and I just warp out and do a different STF.
I was assigned as chief tactical officer for OP's Cure training run and our redneck newbie assault task force blitzed through the mission so fast that after the assimilated carrier blew the loot spawned but not the mission complete timer.
In all redhead stupidity I said damn the f-ing torpedoes and hit the leave system button after a long wait.
And then I forgot I read about this issue a long long time ago in a forum far far away saying you should log out and back in to evade the leaver penalty.
No biggie, I took my cadet through a 1 hour ground training session and did a redneck style Kitomer Ground later :3