Whoah! That's a new one to me... (single player anyway) I'd like to see if it can be duplicated. Please post your hardware, OS and OP mods installed.
This issue is known in split missions, where in a multiplayer mission if a player drops or fails to connect, but is flying their own version of the mission alone, usually all the fire is double from then on for the remaining players. (Double DV shift too, so sometimes its worth risking finishing the mission)
Best advice to avoid this issue is not to use software firewalls, wireless connections, NortonAV, or USB modems. (The trick is, to guarantee a stable mission - all players must follow these guidelines, which is very nearly impossible to achieve)
Starfleet command was developed in those heady days of decades gone by when such agressive security measures were unthought of*, thus there is no code to account for such exceptions, as they did not exist at the time of development. SFC assumes that windows has a real, direct connection to the internet, an uncorrupted TCP/IP stack (which is what software firewalls, Norton AV and internet accelerators do), and untampered windows sockets. Now, quality hardware NAT is accpetable so long as you are aware of the exact networking requirements which I have outlined on these forums countless times. (This is not directed at you personally, this is just my usual rant on the subject.) Note that doing so poses no security risk whatsoever if you know what you are doing, as evidenced by the fact that I have been running the same uncorrupted, unhacked, virus and trojan free install of XP since its release in 2001.
*OK, not unthought of, but at least very uncommon. Back in '99 I installed blackice, a software firewall. It took me some time to figure out why my Dynaverse missions would unpredicatably bug out and lose connection. Often it was fine, but often I'd lose connection. I actually made an ass of myself claiming I was being hacked because of my good playing skills. (Paranoia=Big-Destroya) Eventually I put it together and uninstalled blackice and presto, my Dynaverse missions ran just fine again. Even though I had made all the necessary exceptions for OP in blackice. I have observed similar effects with ZoneAlarm. And you might as well forget it if you're running 2 software firewalls. Anything that screws with your networking can be a problem, and intermittent. Just becasue one mission (or even five in a row) works with paranoia software on, it does not mean the next one will.
Did a player drop from your GSA match? It's not always obvious. Were all players chatting throughout the mission? (Thus the courtesy ritual of "Hail" at the beginning of a mission and the "GG" at the end, which achieves taking attendance for the mission.)