How does Wade's ship get damaged?

If you're referring to the incident in chapter 23, Wade's ship (the Vonnegut) is damaged after taking heavy fire from Sixer gunships.
In the chapter, Wade is on planet Frobozz, which contains a recreation of the game Zork. Wade is on Frobozz because he has learned that the Jade Key is hidden there.
Once he lands on Frobozz, Wade gets to work completing the game of Zork. He finds the nineteen treasures and places them in a trophy case. Then, he blows the Cap'n Crunch whistle he found in a cereal box in the back of a cabinet. The whistle then transforms into a Jade Key, catapulting Wade back into second place (one thousand points ahead of Aech).
On the key is inscribed a saying: "Continue your quest by taking the test." While Wade is pondering the meaning of the inscription, he hears the roar of Sixer gunships in the sky. Immediately, Wade makes for his ship. He gets there in the nick of time and takes off. Luckily for Wade, his ship is fast and boasts cloaking capabilities as well as strong defense shields. Despite this, Wade's ship still sustains terrible damage in the hull from Sixer gunfire.