99% of the time,, "rust" on stainless comes from "transfer".
Steel will transfer onto stainless steel,, just like the paint is "traded" on the cars during a NASCAR race.
During manufacture, steel tools are used to make the stainless steel part.
Some of the steel from the related tooling can become attached to the stainless steel part.
Usually, the stainless steel part is dipped in acid to etch away any steel.
These spots look like steel that eluded the acid bath.