I had this happen to me a few nights ago. Queued up for ISN and was dropped into a game that had already lost the optional and one transformer was already down. Someone must have dropped out for whatever reason so it slotted me in. It it would be nice if the queue would give you the option of whether or not you want to join an already running STF.
* Missing - Bridge Officers. If found please return to Admiral Quinn!! *
Bug has been around awhile, sometimes avoidable if there's only 3 in the queue and you get prompted to 'Engage or Leave' anyway. Maybe they could at least add a catch exemption to the leaver's penalty if you get dropped into one like that, as the main bug seems non-trivial to fix considering they haven't already fixed it.