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: One of the defeat/death lines of the AI enemies is "This unit has completed it's mission." Whoever programmed the AI, programmed the grammar wrong (should be "its mission").