New tech products are often plagued with software bugs and the like, so it's no surprise that there's one with the iPhone 3GS. That said, this is the first bug I can remember that actively targets dogs ears: Updated
You see, it seems that some iPhone 3GS smartphones are emitting a high-frequency tone—something along the lines of 15KHz—that's triggered when the unlock sound, or SMS sound, finish playing.
BGR confirmed this bug with their phone, and others have piped in to say that they too have handsets that produced strange sounds only a dog could hate. This appears to be software-related, and patch is undoubtedly forthcoming.
Meanwhile, you might have this bug and not even know it, as the tone is apparently too high for some older folks to hear.
Update: Your dog is safe, but this tone is still annoying some people. [BGR]