Why is there a phase difference in common emitter configuration?

The phase shift from input to output is 180 degrees, which is just another way of saying the signal is flipped in polarity. What the phase shift means is that as the input starts going positive, the output starts going negative. The phase shift is due to how the device works in that configuration. Let's say it's operating in class A where the device is never cut off or reaches saturation during a full cycle of the input. The base is static biased to have the device running in the middle of its operating curve. It idles as some nominal value of Ic and awaits an input signal. When the voltage on the input starts to go positive, the device is forward biased even more than it was at idle. As forward bias increases, collector current increases. That's how the device works. Turn it on more, and more current flows through it. As collector current increases, collector voltage decreases. There's the key. Increasing base voltage causes increasing collector current and decreases collector voltage. Increasing base voltage causes decreasing collector voltage. And the opposite is true. That's it in a nutshell. Common emitter configurations phase shift signals by 180 degrees. And now you know how they do it.