there ARE a couple oddity motherf*** missions in FSPort that are difficult due to the missile handling. One of them is the 3 freighters carrying the shield prototypes, and the other one involved escape pods if i'm not mistaken. basilisks jump in and immediately dump a f**kload of missiles at your objectives before you have any sort of opportunity to kill them.
The shield prototype mission IS harder in Port than FS1, the best you can hope to do is put the missiles off and make sure you're over the jump points.
Failure to communicate isn't too bad so long as you handle the dragons immediately (I normally tell the AI to ignore the dragons and protect the escape pod that's at the front of the little convoy, so that I can knock them out immediately with Phoenix V (they're a lot easier to hit from directly infront or directly behind at the very start of the mission because they don't try to avoid the PVs very often, and the PVs oneshot them).
When the Basilisks jump in, if you dispatched the dragons fast enough you should be back with the pods already, - hit shift-e and then 3, and go hell for leather on the basilisks, then tell the ai to fly with the first escape pod again, and repeat twice.
You should get the bonus objective for that.