Microsoft acknowledged that there are indeed damaged Halo 3 Limited Edition Game Discs and Essentials Discs and will replace them free of charge through 12.31.07.

However, it may take up to two weeks for Microsoft to send you a proper replacement, and the offer is valid only if you purchased the game through a legit retailer. Ordinarily, gamers would have to pay $20 for a replacement disc, but since Microsoft acknowledged it's their fault, they are doing it for free.

Halo fans were outraged when just hours after the Halo 3 launch it was clear that there was a widespread problem with the special limited-edition packaging, as it apparently was scratching the video game discs. The Limited Edition is the mid-version of the game, which comes in a tin decorated with the "Halo 3" logo and costs $10 more than the normal version, which is $60. The top version comes with a replica of the helmet worn by game protagonist Master Chief and costs $130.

Apparently the Halo 3 game disc and an "essentials" disc were coming loose during transport from their plastic housing designed to keep them in place. The discs were getting scratched but most users were still able to read them without problems.
You need to fill out this form if you want the discs replaced:
http://assets.xbox.com/en-us/support/replacementdisk_orderform.pdf

Microsoft announced a variety of new merchandise, related to its Halo 3 launch, including two new Xbox 360 Limited Edition “Halo 3” Wireless Controllers designed by Spawn and McFarlane Toys creator Todd McFarlane, as well as an Xbox 360 Limited Edition “Halo 3” Wireless Headset, which lets gamers talk with friends over Xbox LIVE.

Also a special Xbox 360 console went on sale alongside Halo 3’s September 25 release date. The console features an authentic Spartan green and gold finish and comes with matching Xbox 360 Wireless Controller, 20GB Hard Drive, Headset, Play & Charge Kit, HDMI output and exclusive Halo 3 Gamer Pics and Theme available via Xbox Live download.

Either way, Microsoft and Bungie have set the standards high before launching Halo 3 and apparently they’ve kept their promise to deliver the ultimate Halo experience to eager fans. It remains to be seen whether this peak (translated into higher sales for the Xbox 360) will be followed by another massive drop, with Halo 3’s halo outshining all other FPS titles, or whether titles like Call of Duty 4, BioShock and Jericho will be able to keep up and drive sales after the Halo hype has faded out. This fall is filled with enticing, multi-platform titles (including the astounding PC game Crysis) and without the Halo 3-exclusivity the Xbox 360 would have certainly lost the fight.