In one scene Janet signature is on the card but when Velma turns it around the signature disappears.
Elliott Blender is miscredited as "Elliott Blinder." Additionally, the closed captions also make the same mistake, and also refer to Velma Dinkley as "Velma Dinkly."
As Daphne is chased across the gangplank, in one shot the railing is different than it should be (not spanning the entire length of the gangplank).
Velma refers to the organization as E.T.I.S., but the logo around the base has "S.E.A." written underneath it.
After Velma says they need someone to lure the alien to where the trap is, the background behind Shaggy and Scooby is of the main hall where Velma received her award earlier, not of the room where the centrifugal force machine is located.
Fred is missing his eyebrows when Velma tells the rest of the gang that Janet works with E.T.I.S. at the base.