We have noticed the same issue on our servers. Running a moderately large mission (with no carriers present as it happened to be)
I was buddy lasing a target for another player, they were trying to hit a moving convoy on the ground. It appeared that the players aircraft was about 200m off position for the convoy. They released their GBU-12 and it seemed to travel about 200m to the east of where the target was. When the bomb hit the ground, it exploded. But so did the truck being lased 200m away from impact point. We also had issues with GBU-38's hitting about 100-200m off target in a seperate mission on the same build. I was giving precise coordinates for the ground vehicles, but the bombs would always miss by 50-100m (these targets were stationary however). It appears that ground vehicles are indeed desynchronised between clients
Hopefully this helps out a bit. I can provide more info if needed
Server specs: I7, 32gb ram, plenty of up/down bandwidth