I'm playing vanilla TFTD with the latest nightly. An Alien Infiltration mission began in Indian Ocean and all the usual USO's spawned including both Very Large ships which should have meant that the mission was successful for the aliens. For some cash I knocked out both the landed Very Large ships and the Supply ship with ground assault. The remainder flew away unmolested and at the end of the month no new country had signed a pact and no new base was created.
According to the wiki the aliens should have fulfilled the mission once the larger ships spawned. All you can do is delay by shooting down the scouts. This has always been my experience as well. I'm wondering if what I encountered was a bug or were the rules changed? Just curious, possibly it's a good thing to give player a chance at stopping these missions.