I've not been on for abit, but here's two things I've been sitting on trying to figure out for awhile, someone might've got there first though.
A: The UEF Alarm klaxon. Why does it revert to the GTVA one (as seen in AoA) rather than that used by the Renjian at the end of AoA?
B: In Delenda Est, if I remember correctly the Carthage 'snags on Jupiters gravity well', pulling it out of subspace. If it is incapable of re-entering, why are it's escorts capable of jumping out alongside it while the other ships have to climb free?