Why is my Android phone off by 3 seconds only a few minutes after I set it to the Atomic clock time? I have a Huawei Mate 9, and just set it to the atomic clock time a few minutes ago. The ClockSync app reported it was off by 0.06 second at that time.

However, a few minutes later when I picked up the phone and check again, it was already 3.2 seconds behind. How come it can be off by that much in a few minutes time? Doesn't the phone has an internal clock which should be only off by a few seconds in a day?
Time on devices is an approximation based on the molecular activity of the components it is constructed of, especially mineral vibration. Some components and the software that estimates from it is better than others. Better phones with better components, or, better phones with better software are necessary for best time estimation. If the estimation is off for you, leave the setting for synchronizing time from the network. The responsibility of your device to perform flawlessly is reduced or eliminated.

See this article online which details how clocks on devices work.