One of my systems was getting assaulted by a CPA and had my engineers building a MRS, when it was done I tasked them to repair the FF generator (which they did, once it reached ~7 seconds after it was last damaged, and in one they repaired it from 10% to full).
Then they decided that they'd help repair the fleet. "No! Come back, under the FF with you!"
They left.
Back I called them.
Gone.
Back.
Gone.
Back, this time the FF gen again.
Fully repaired, gone.
Dead.
They simply would not obey an order to SIT TIGHT. It was like they were on permanent Free Roaming Defense. This is not expected behavior, I wanted them out of the combat zone (that's what the MRS is for!) and they refused to do anything but go out and get hit with a flood of electric shuttles and die.
Le sigh, there went the two Mk2 Engies I captured...