These two missions need to be tweeked for Battlecruisers and Carriers.
You don't have enough DPS to fight the Patrols and disable (and loot) the transports at the same time. Even with Warp Plasma to snare them. And on top of it, if you blow up a transport, the mission becomes a failure.
So it's quite frustrating to put all that time in hoping for 5 emblems, but end up with 1 or 2.