Plot hole: When Shoji gives himself up to the authorities at the end of mission 9, Aoki thanks to the Senpuji Industries lies to the inspector saying that he was a test pilot, but that does not solve the not marginal issue that the playing character comes from another dimension and has no ID. The inspector is a stickler for the rules but in all the hours of interrogation apparently the subject of their identity never came up.
Other mistake: At the end of the 6th mission, the assault on Pluto, the capital ship led by Schultz escapes. Before making a run for it, it says "Full speed ahead! Destroy the Yamato!", which is probably a mistranslation, since there is no attempt on destroying the Yamato, their reason to move 'full speed ahead' is to escape and in fact any surviving force is retreating together with him.