Star One (spoilers)
I've seen all of B7 a few times now and I did really enjoy Star One but so much of it made no logical sense.
1) The Liberator is the fastest ship and far faster then Federation ships. It took the Liberator a really long time to reach Star One (and in one shot you see the milky way FAR away which means they are between the galaxies) yet the entire federation battle fleet arrives in time to join the Liberator to defeat the aliens.
2) What was the minefield protecting? If it was Star One, how did the aliens take over in the first place? It can't be around the entire galaxy. Space is really big. If you know where a minefield is, you just fly around it.
3) Everyone kept repeating that if you control Star One, you control the Federation. But the aliens, who managed to not only take over Star One but extract all the technical knowledge required to operate it, took quite a while to just disable a portion of the mine field.