Character mistake: One of the possible messages that happens when Yamato faces Le Chevalier during mission 7 ("Cosmic Crossroads") prompts Kodai to say "This is the ship that is guarding the Pluto base." It's a phrase that fits their previous encounter when Shulz was in fact doing that, but since then the Pluto (or "Plato" base as the Gamillans call it) base was destroyed (by the Yamato itself, even) and they moved past it.
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").