First up, there is a disclaimer that appears at the start of the film right after the copyright warning. This reads:
This something that I've not seen before, but post September 11 nothing comes as a surprise any more.
The second issue is the omission of the words for the Vandals song Anarchy Burger (Hold the Government) as sung by Xander and Yorgi. While the words are clearly heard, the subtitles completely drop out until the singing is done. The passage is:
"America stands for freedom, but if you think you're free
try walking into a deli and urinating on the cheese."
Thirdly is the issue of the blurred faces of the 3 girls on Yorgi's bed in deleted scene 7 in the Xander Zone Deleted Scenes section of the disc. I couldn't find any reason that the faces were obscured. Lastly is the removal of the headbutt that Xander gives to one of Gibbons' men just after the raid on the Colombian drug farm. While the Region 2 UK disc cuts this (about 1 second by all reports), the Region 4 disc preserves this scene and it is intact.