I've run into the same problem....can't attack any transports or couriers in the Regulus sector. Only trade. Any feedback anyone?
The convoys that are attackable - all have a couple of NPC Fedration ships flying in formation near them. Also, if a battle is ongoing, it has the same Black/Red swirling graphic but says 'Frieghter' when you get close enough.
Also, currently, completing the PvP version currently DOESN'T count for the KDF Sortie mission. If that's by design, hopefully they'll have a 'wrapper mission' for the PvP version.