Scott Vernon's failure from 12 yards carried echoes of the previous Sunday when the same sides met at Pittodrie in the Clydesdale Bank Premier League.
On that occasion Niall McGinn was denied by Ben Williams, and Brown believes those two wasted opportunities define the Dons' stuttering season.
"If we did not miss those two penalties then we would be fourth in the league and still in the cup," said Brown, whose side have gone four league games without a win.
"These are the fine lines between major disappointment and a bit of success.
"But I can't fault my lads for effort and application. We bombarded the Hibs goalmouth.
"When you hear their goalkeeper is man of the match, then it tells the story.
"We should have won the game, let alone got a draw."