I have NEVER afk'd an STF, NOT ONCE !
Yesterday, TWICE separated by half a dozen hours I crashed to desktop during Crystalline Entity normal, and BOTH times was firing at a recluse.
1ST time, had many minutes of normal destruction before crashing out of mission. I took the time to submit a crash report and on relogging found myself in an empty CE instance with no reward - NONE. So I took it in stride and sucked up the loss of time, rewards, and cooldown till the next time I could run the mission for much needed fleet marks.
2ND time, early this morning before bed I had just buffed for an alpha strike on my first target of the mission and just as I get into range, CTD. I quickly relog forgoing the crash report only to find myself in the closing seconds of the match unable to control my ship of fire my weapons, and watching the entity get killed. Again no reward. On exiting the instance normally I find a 2 hour AFK penalty timer at the bottom of the PvE menu and I'm unable to join or start ANY PvE mission.
This new issue (and feature) is a bit of a double-whammy for those playing in good faith but getting punished for funky coding with this new expansion. I guess I shouldn't be surprised as I had to drop TWICE this weekend the fleet daily where I have to inspect some recruits and a recruit either has no issues to correct or has an issue that the correction doesn't allow the mission to proceed (ALWAYS with the boots). This is an issue that been around since the fleet system was introduced.