The first time SpyFox exits the fortress through the town square entrance, the hanging lamp below the secret elevator is crushed. If that's how William the Kid got in (before SpyFox), the light should be crushed already when SpyFox enters the room for the first time.
Bug: In the American version of the game, the Spy Trap coin is made to look like the back of an American nickel. The British dub changes it to a silver version of the British penny. If you force the British dub into fast mode (done by entering "ForceMachineSpeed=Fast" into hegames.ini or scummvm.ini) and scroll through the gadgets in the Spy Gadget Vending Machine, the gadget will appear in its American form and change to British a few seconds after you've stopped scrolling.
Bea tells SpyFox that Sal comes to the Cantina every day directly from the boat, and that he shows up "## minutes after the start of Happy Hour." Even after SpyFox sets the boat clock to that time, Sal won't leave the bridge until his replacement (whom SpyFox impersonates) arrives. Thus, it's reasonable to say that Sal's arrival time should be different each day, and Bea shouldn't be able to give such an exact number.
William the Kid's secret fortress is either under the ocean far away from the island or a good drive from the town square. If that's the case, how is there a secret entrance directly from the town square when the fortress is walk-able? In other words, SpyFox shouldn't be able to walk from the snapping turtles/underwater end of the fortress to the town square end AND have to take a car/boat to the former when outside.