If he was a bit rough, the brown discharge could just have a bit of dried blood in it. That's fairly normal, and unless it smells or persists for very long it should be fine. Just keep an eye on it! A bit of bleeding after sex isn't dangerous in itself, but could make you vulnerable to infection (yeast etc), so I'd suggest using a bit more lube during rough sex.
As for the delayed period, I'd guess that stress is the likely culprit, and focusing on eating and sleeping well is probably the best cure :)