This is called the Book Sea Battle Method, something the civil servants of the Outer Court love to use. Some matters, when they don't want the Emperor to know, yet cannot avoid reporting, can only be handled in this way. The Emperor is but human as well and will have times of fatigue. It's impossible for him to know every minor detail. Trying to manage everything and know everything would certainly shorten one's life.
However, regarding Prince Yu's presumptuous actions, Chen Zhong specifically placed them in the most conspicuous location. There was no other way; his loyalty to the Emperor is as clear as day and night, and he would never commit the heinous crime of deceiving the Emperor for Prince Yu.
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