Thanks for the response - Steam tells me I've put in 20 hours of game time so far, I have touched the game quite a bit, even sometimes inappropriately.
I just have a perfectionist streak that has made me restart the campaign around 4 times now.
I'm certain I've made the Tonnage-counter for objectives move even while not on the mission for that objective during a particular patrol. Grabbing a merchant in passing while hunting for the carrier, for example, made the 100k goal move. If that wasn't the case, what would be the point of the "patrol your area of choice or return to base" message? (I'll gladly stipulate that there are some missions where this doesn't come into effect, but "kill x tons of merchants" isn't among them)
Is it possible that the carrier group is also way more spread out than the normal patrols are? I once encountered a group of destroyers in a very, very loose formation in the target area, loose enough that I could sprint to the middle on the surface without detection, but there was nothing in the middle of them.