I ran into this issue today during the Wolf 359 task force. Two Assimilation probes got stuck in different sides of the cube. You could target them but seems like all weapon fire and aoe damage wouldn't work on them. One person from the team left, I backed off got out of combat and changed skills. Thought maybe tractor repulsors...nope nothing. Then Eject Warp Plasma... that got them. Then the rest of the team and I finished the mission.
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