Are you talking about the physical AppleTV remote or the AppleTV remote for the iPhone/iPod/iPad?
Originally Posted by G323Q569
If you're referring to the physical remote that came in the box with the AppleTV, try pairing it with the AppleTV. Out of the box, the remote is not paired with the device, and the remotes and devices will work in any combination with other devices unless they are paired with a single device.
That said, I wasn't aware that the iPhone had any kind of receiving port that could be activated by an IR remote. But if it is behaving as you say (not doubting you, just never heard of that before), pairing the remote with the AppleTV should cause it to only work with the AppleTV.