Why do consecutive tripod shots from a phone shift by a pixel or two?

Small pixel shifts between consecutive shots are normal, especially on phones. Modern phone sensors have extremely tiny pixels, often around a micron, so even a microscopic movement can shift the image by a pixel or two. That movement can come from many sources: slight tripod settling, residual vibration, internal stabilization or autofocus elements, or even handling the setup nearby. At that scale, “perfectly identical” frames are very hard to achieve in practice.

So yes, trying to get two completely identical captures is usually unrealistic. If you want the closest match possible, let the setup settle before shooting, use a remote or self-timer, disable stabilization if the device allows it, and avoid touching or moving near the camera. But a tiny translation of a pixel or so is not unusual and does not necessarily indicate a problem.