The foal is definitely brown- which means that either the sire or dam (or both) are actually brown, and not black. Since the foal is registered, parentage should have been verified, so that rules out the sire not actually being the sire.
From the pictures, it's a toss up as to who's brown and who's black with them. Stallion owners will often have their horses genetically color tested since people often want to know the color genetics before selecting a stallion to breed to, so you could check with them if they did an agouti test and not just the extension (black) test. You could easily test your mare as well; you just pull a few mane hairs and send them in with $25: link