I wonder if it's actually that this bug is happening more, or for some of us it's getting to the point where the few Enemy Encounter secure systems we haven't completed and bugged up already are the ones that are bugged and not completable.
I met Jeska two days ago and went through great lengths to lure an enemy ship within her range, to see if she'd attack it or get attacked. Neither. She just happily flies in torpedos and takes no damage, and beams go right through her. I believe its a fata morgana ship.