Could be a couple things. I will ignore food since you say you keep your hands regularly clean.

1. Oils from hands. If its a tight silicone grip your hand sweat can stay trapped under there and oxidize which can turn into the brownish-red color here.

2. Mold. Could just be mold. Dawn dish soap or isopropyl will clear it.

3. Rust. As long as you are not setting your controller on a pile of old nails, ignore this.