Why does a turbine engine compressor ratio affect stagnation pressure?
By stagnation pressure I assume you mean total pressure. Stagnation is not a term commonly used in gas turbine engine performance, it’s more common with aerodynamics. The compressor increases the total pressure because the rotating blades are doing mechanical work on the fluid. 

A couple of other comments, to explain in more detail;

First, the flow is not isentropic in a compressor. It only would be if a compressor was 100% efficient. The efficiency is actually calculated by the degree to which it is not isentropic. The efficiency is given by the isentropic temperature rise that would occur for the given total pressure rise, divided by the actual total temperature rise. An efficient compressor obtains the same pressure rise, for a smaller temperature rise. While you might think a higher exit temperature would be good, because it would mean we could burn less fuel, a greater temperature rise across the compressor would require more shaft power to compressor the air, which is taken from the turbine and means the turbine exit gas is now cooler and a lower pressure and now cannot produce the same thrust.

Secondly, the stagnation pressure is not constant (even if it was 100% isentropic). This maybe the case in a fluid flow where no energy exchange is occurring, but in a compressor, the rotating blades are doing work on the fluid. This increases its total pressure. The area at the entrance and exit determine its velocity (along with its density). Different areas, changes in density, and total pressure mean the static pressure isn’t the same at the entrance and exit, either.