Bug 1) Gunboats and larger ships can't "dock" with the Landing Pad during Paradise Lost.
This likely isn't a problem for most, but since I am... less than good at the game I die pretty quickly if I use anything less powerful than a gunboat after the last of the Vanilla missions.
Bug 2) During the Liberation of Sol it took a couple of retries for the battle with the Nomad battleships to happen, and when it did the Osiris was 300KM (roughly) away from the battle. All in all, though, thus bug was just an annoyance.
Bug 3) Crashes here and there. Nothing preventing me from doing the Crossfire-related story missions, though, so it just used up time.
Bug 4) Waypoints can't be placed post-Vanilla Story Missions (unaware if a bug or just not possible for technical reasons).
Off-Topic: Is the Adv. Brigandine H. F. Shield Mk II the biggest capacity Elite shield obtainable pre-Paradise Lost?