Bombers in low numbers/squads tend to have major difficulty hitting the Vaygr Shipyard capital ship facility. They aim right in the middle of the opening, thus providing damage to the shipyard and not he facility. Other ships, when attacking it from above, will have similar issues, though not as consistent.
At first, I though it was just a fluke, but after two games of the same issue under similar techniques used, I think there is something else to this.
A possible solution would be to include a facility ‘floor’ or hitbox inside. This would cause all damage that enters that bay to cause damage to the facility, which would make sense, as that entire part of the ship (the blue building bay) is used for the purpose of building capital ships only.
Other solutions would be to move the target point out of the center, or alter attack patterns.
I don’t know how difficult those suggestions would be, though.