Realize that Kerosene (RP1) is not the cleanest burning fuel.
Also, this stage has not just ascended up through the atmosphere, it has re-entered, taking in a fair bit of heat along the way. So some of that is likely burnt paint.
But as it does this, it is flying tail first, through its own exhaust plume. This is mostly just burnt kerosene residue that comes from flying through 3, then 1, then 1 engines thrust (175 klbs of thrust each engine) which burns ALOT of kerosene when running.
You can see where the outlines of the legs go, still being pristine and white. They stay closed till about the last 8-10 seconds of flight.
Also, there is suggestions that the LOX tank forms ice on the outside, that persists and protects some of the paint till it melts or falls off. Which can account for some of the odd patterning.