I'm glad Looschey spelled it out for people. Some players want more strategy but are not willing to maximize the strategic options available now.
I'll try and explain it from another angle:
Damaging factories extend the time its corresponding base or town object is down. All the factories to base OBJ relations are obvious (AAA factory = auto ack, radar factory = radar tower, etc). The city effects the down time of the HQ and town buildings. None of the strategic factories or the city are intertwined, they are completely independent.
Regardless of the length of time OBJ's are down for on the field, delivering a field supply will remove 10 minutes from the total amount. ANY of the repairable OBJ's within 1 mile of where that field supply is dropped will be repaired. Hangers may not be repaired, they are down 15 mins regardless.
Each truck destroyed adds 54 seconds to the down time of destroyed OBJ's on that field or town. There are 8 trucks in the convoy and that means a 7.2 mins (7min and 12 sec) is added on. The barges are worth 1.6 mins each (1 min 36 sec) I believe, there are fewer of them but I don't remember how many (5?). If there is an enemy tank armed with HE sitting near the convoy route, that tank alone can increase the down time of the field strategic OBJ's by roughly 30% over a given period of time (every ten minutes as the convoy passes by 7+ minutes can be added if the entire convoy is destroyed). btw, it takes roughly 80 lbs of ordnance to destroy a convoy truck, more for a barge but I dont remember atm.
With regards to the OP's situation, it may be a case of partial destruction of the convoy. I have not looked at the numbers close enough. It certainly could be a bug.