Daphne is barefoot while in the Mystery Machine, but when she gets out she is not only wearing her shoes but also her full-length stockings/tights.

When the ghost pirates attack the Galaxy Gazer at the beginning of the movie, Rupert swings his door open into the passage outside. When he sees the pirate ship with cannons at the ready pull up beside, he backs up and slams his door shut from the inside.

Skunkbeard's ship's size seems to change from colossal (while grappling the cruise ship) to the size of a small brig (during the last scenes). A ship from that time period would certainly be nowhere near as large as a modern cruise ship.

When Daphne is first in view in the Mystery Machine, she's clearly sitting regularly, but when it switches to up-close, she's in the middle of painting her toenails.

The vessel is first shown as Poseidon's Paradise. After it's out of dock, the name disappears, and from then on its simply referred to as Poseidon.

When Scooby opens a pot, a lobster pinches his nose. The lobster is red, and lobsters get their red color after being boiled. Live lobsters are a dark greenish-brown color.

When Skunkbeard and Wally are searching Rupert's modest-sized quarters for him, what are the odds they wouldn't look under that bed?

The USS Cyclops is said to be missing for over 100 years. It launched in 1910 and disappeared in 1918, much less than 100 years before 2006.