This mostly has to do with the UEF Engineering station, but I've had trouble with the Cybran one as well. I've seen a couple of issues with their behavior:
Problem 1: I start a building but then change my mind, I want something else there. So I tell the engineer to reclaim the building. I come back a minute later and realize that a nearby ES has repaired it.
Proposed solution: When you order an engineer to reclaim something, mark that object as "do not repair".
Problem 2: A few bombs or artillery shells make it through the shields and damage some buildings. I quickly check that the ES's are still intact, they are, so I go elsewhere. I come back later and see that nothing has been repaired -- the ES's have been stuck helping an SML reload for the last couple of minutes.
Proposed solution: Prioritize better. Repair things first. Assist factories second. Build missiles last. They should be able to change targets without waiting for the current target to finish, so they can immediately go repair as soon as the damage happens. If that's not possible, maybe make it so they CAN'T assist SML's? Their contribution there is insignificant, it's far better to leave them free to repair damage as soon as it happens.