It happened to me (I noticed it happen on the map Trainyard) that when doing the ‘secondary objectives’ missions I didn’t have to fully repair the side generator.
I just did a little bit of repair but was interrupted by an opponent so I had to let it go and fight. I didn’t have the chance to go back and finish it, a team mate did it, but nevertheless it counted towards the mission.
It looks like a bug because I only repaired a very small percentage of it.