A 2-0 defeat saw the Dons' wait to score against Hearts extended to eight matches, the last strike coming in January 2010, as Ryan Stevenson's 31st-minute penalty and Callum Paterson's goal gave the hosts the points.
Aberdeen were frustrated by Jamie MacDonald, who made a number of sharp saves, and Brown said: "It's just one of those things.
"We inherited a situation where Hearts were beating Aberdeen and we've not managed to redress that."
Aberdeen substitutes Jamie Masson and Declan McManus came closest to finding the net but Brown, whose side meet Motherwell in a Scottish Cup fourth-round replay on Tuesday, added: "The two young lads are distraught. I could have run from the dugout and scored."