A piece of malicious software on a system could certainly make specific discs appear to be bad or unreadable. But as far as corrupting the actual physical media on a non RW disc with a non writer drive, not possible, or at least I've never seen it in my 10 years of being a certified MCSE/MCSA. If it's a Win dvd directly from MS (ie, not a home written disc of the DVD-RW variant), there should be no way in hell it would have been over-written by a DVD reader. If it was an acquired copy that's non-OEM on the original disc, it could very well have malware on it if you have autoplay enabled, would have installed itself the moment you inserted it if you are not running the latest Win security patches (USB sticks can do the same on older Windows machines lacking the latest updates). The Sony BMG rootkitted audio CDs worked in a similar fashion.
What is the name of the software culprit you discovered, and I assume you tested said disc on other systems?