Rust:
May well be surface rust from water with an iron content.
Begin with cleaning the area with one of the rust/lime removers like CLR or Lime-Away. Rinse well afterward.
If you see obvious sources of rust, then there are ways to deal with them. But do the simple thing first, and try not to worry yourself into worst-case scenario before it's absolutely necessary. A lot of "rusty" sumps are just stains from water.
Also, that bottom rack was replaced for a reason, and the reason was almost certainly rust. So, the rust staining in your sump could well have come from that.