This might indeed be some editing mistake or something changed later on to make the whole thing a bit more cruel and less like "they let him die, but we could help him".
Re-watched that part of the movie and there's one short screen obviously showing the submarine's radar or sonar or whatever (assuming that due to the short cut before showing the submarine's back):
As you can see there are exact five targets. Two of them almost overlap, so look at the circles on the top/surface. The contact on the left might be the freighter we saw earlier, considering it's not underwater and not marked in red.
Only possibility I could think of would be the small "doc bot" counting as another signature, but that wouldn't make any sense considering the targets are obviously counted in ascending order. Megatron obviously received designation "C-6", but why are "C-1" through "C-5" still with him? Maybe they didn't kill the Construction(?) after all? But where did they get the spark from then? Or did they pull him on some kind of cable? But why does he still show up, considering Megatron obviously didn't show up before (otherwise he'd have a known signature I assume).
Edit: The whole "opening" of that sequence includes quite a few mistakes. After all, there should be five Constructions (and that's the thing that disturbed me the most when first thinking about the whole sequence):
First scene: There are four Decepticons visible: wheel loader, cement truck, caterpillar, and some green truck.
There comes the cat-like/panther robot. Especially note his path, he's going to hit the front of the caterpillar. Also remember the position of the vehicles relative to each other.
The next scene shows the actual impact. The mixer truck is further back and the wheel loader is now a bagger(!?).
So initially there are five Constructions (or another goof/mistake) and the panther? But wouldn't that make six contacts to start with? And we only see four jumping into the water? It's easy to miss, but the panther jumps first:
The next jumping are (some random guessing included): bagger, mixer, caterpillar, truck
According to IMDB there is one more error in these scenes:
When Megatron is coming up, the Captain calls for hard left rudder, and the sub's rudder turns right.
But they've got an explanation for the 5/6/5 discrepancy:
When the Decepticons go under water to revive Megatron, the Navy states that 5 "objects" went under water. If one of the Decepticons was killed to bring Megatron back to life, 6 "objects" could not have come out of the water: Ravage spits out the Doctor Robot (5+1=6), one gets stripped into parts (6-1=5), Megatron gets reactivated (5+1=6), and Ravage swallows the Doctor to head back to the surface (6-1=5).
This just doesn't explain Megatron having a "new" designation, while one of the others doesn't.