Bug: In the Mars Lighthouse, in the same room you defeat the Flame Dragons in, return after you have defeated the Flame Dragons and fire off the cannon. A crack will appear where the ice was, even though there is no ice.
Continuity mistake: When you first meet the Doom Dragon on top of the Mars Lighthouse, its red head is on the left. When you actually battle the Doom Dragon, its red head is on the right. You see it both times from the front, so it's not an angle issue.
Plot hole: Even if you've acquired Piers's ship before visiting Garoh (a city populated by werewolves), when you first set sail in Piers's ship, Sheba will say, "We've already met werewolves."
Other mistake: The description of Alastor's Hood states that it can be used to Haunt a foe, however when used, it will attempt to Condemn a foe for an instant kill instead.