Hi DEMO,
I think you're experiencing a feature which I personally find useful. ATV is not responding to IR commands from your TV remote. Instead, your TV is actually controlling ATV using the HDMI-CEC feature. This allows the TV remote to control connected devices, like DVRs and DVD players. I find that mine sends the arrow navigation keys, the enter button, and the return button to ATV. These let me browse the menus and control playback without reaching for the Siri remote. Oddly, the play/pause buttons do not affect playback, except in the YouTube app. There seems to be no way to stop ATV from accepting these commands. Turning off "ControlTVs abd Receivers" doesn't do it. Your only option is to turn off HDMI-CEC on your TV. Note that it has many different names, just dig through the TV menus. But if you try it, you may find you like it. Certainly, there are some TV commands you must avoid because they also affect ATV, but I like it.
And by the way, for anyone wanting to exploit this feature, ATV seems to ignore the commands unless you start with a few moves on the home screen using theSiri remote. Then confirm that the TV arrow keys work. Then they will continue working. The TV enter key is rhe same as a click on the touchpad, so it works as play/pause.