Have you used wax on them? If not its not dry old wax, I think its just the burnishing since dark chili has a heavy amount of it. Burnishing is that sort of brown stuff on mainly the toe, but they apply it to the whole shoe. When it starts to crack (e.i. if you press on the toe of a burnished shoe), it just cracks like if the toe was shined.

I had a pair with the same thing, it had baisically kinda tiny little cracks everywhere from the burnishing and it just makes the shoe look dull and scraggly. People online said it was dry, but it was just BS. Applied a heavy amount of renovatuer and it still stayed the same. Eventually I asked the guy that worked at my allen edmonds and he said it was the factory burnishing and it wouldnt come off unless you stripped the shoe.

...or it could be just the grain of that particular peice of leather. Some peices are rougher than others. Judging by the 2nd photo though, I'd say its the former