CE amplifier circuit gives output voltage that is not completely out of phase
There are many capacitors you are ignoring, and though most are negligible, one isn't.

Think very hard about what your collector load is. Is it 4k? Is it 1k? Try increasing R5 and go again.

Once that is sorted, you might want to calculate the amount of phase shift the other 10uF capacitors are introducing.

One last capacitor whose effect you won't see until you raise the input frequency is the Miller capacitance of the transistor, between base and collector.