1. All problems associated with in game saves. Stuttering time compression, eternally waiting (Please Wait) for the game to load after the "loading" screen is finished, totally changed tactical situations after loading a save.
2. The "Patrol Area x" mission objective that can never be accomplished. I.E. After completeing your initial mission objective you are told to patrol a new area, and after dutifully mucking about well within 100nm of the center of the designated area for days on end, and after sinking numerous enemy ships, the mission is still unfullfilled.