Unless the commander got multiple crits on the Illithid, or you started in stealth mode and didn't realise the turn order was progressing without you (if you're sneaking when the cutscene plays, combat moves rapidly without your input once it ends, unless you're seen and thus enter initiative), there is no realistic way that either of the boss characters can die short of 4 rounds, which is the most it can take you to reach the transponder if you just run straight there. If the commander crit the Illithid multiple times in only three rounds worth of combat, then that's very bad luck, but it's also extremely unlikely.
