Ceramic Capacitance aging
You must pick your capacitor technology bearing in mind your intended use. 

X5R (Or worse Y5V) is not really the smart choice for filters (Which is what you have if you care about phase shift thru the cap), apart from anything else you will have built a voltage controlled phase shift network as applied DC across that cap will cause SIGNIFICANT changes in value (This gets much worse with smaller case sizes).  

C0G is generally ok for this sort of thing, but you will struggle with finding more then about 100nF or so. The other option is film or maybe a bipolar electrolytic (If going here make the value LARGE, so the phase shift is negligible over any reasonable amount of drift).