I've read on another forum some guys were worried about getting an infection from running cold wort thru the ball valve on their kettle (they were thinking of just cooling the wort overnight and then rack to fermenter then next day.)
I've also noticed I still had some crud in my siphon hose after I had thoroughly cleaned it. I replace those more often now
If it's an infection, it's in one of those two places.
Good luck and let us know what you figure out
Im real careful bout anything that could be left behind (or at least I try to be). I clean everything on brewday and I put a small brush down through my tubes and small places. Completely disassemble my valve assemblies (what I can). Everything gets soaked and washed with hot water and Dawn. If its cold side equipment, then I soak it in StarSan and drain and dry before I put it away.
"Sometimes Im right half of the time ...."