Culprit of the Missing Trout

[WormFisherman]

Decided to head up to a local wts to try out my new rod and reel. After fishing some new pocket water with no prevail, I went downstream to a pool that is usually teeming with small trout. This pool is really clear, and relatively shallow making it easy to spot trout, so I was confused when i saw no signs of life. Started throwing around a trout magnet, and got hit by a nice sized yellow perch. I didn't measure it but I'm guessing it was roughly 11-12 inches. I was so confused by this catch, because the only fish I've ever caught here were trout, bluegills, and chubs. This brings up two question. 1. What are the red marks on this perch? I was thinking it was some sort of parasite but not sure. 2. How the heck did it get here? And should I of killed it?