Same issues, reported as a bug. From the map, it looks like the Borg are ending up in the small room where you disable the shields for later in the mission. Though watching a cover shield vanish and end up in that room is just plain weird.
Can we atleast get a response from the devs as to when to expect a fix. Kinda a big bug when you not only manage to break some of the end game content but also break one of the first missions of the game, and god only knows what else that hasn't been noticed yet.