India won the second Test by seven wickets before lunch on the final day to take a 1-0 lead in the series, however the game was littered with incidents that overshadowed the cricket.
Zaheer reacted angrily to England putting jelly beans on the pitch while he was batting on Sunday evening.
"It's an incident that has been blown out of proportion," Vaughan told reporters. "A few jelly beans were left on the floor by the stumps at a drinks interval as we got a wicket.
"If it offended Zaheer in any way we apologise for that. But there were no jelly beans thrown from the slip cordon.
"It's not the reason why we've lost a game of cricket, because of some jelly beans. We just didn't apply ourselves as well as we could have done with the bat. We were probably 60 or 70 runs light in the first and second innings."
Vaughan said England should have scored a total nearer 260 in the first innings rather than the 198 they managed in bowler-friendly conditions.
Even in the second innings, when he scored 124, Vaughan hoped another 80 runs could have given India a testing chase on the final day. Instead they required only 73 for victory.
"I felt we had a chance of posting 150 to 180 and we all know that chasing that target, as we saw against Australia (when England won by three wickets in 2005) can sometimes be tricky. That game was in the back of my mind."
The England captain did not feel he needed to speak to his team about their conduct despite several verbal exchanges between opposing players.
India's Shanthakumaran Sreesanth was fined 50 per cent of his match fee for barging into Vaughan at the non-strikers end on Monday.
"The game is played in a tough manner and yes there were probably instances that may have gone over the line, but it's just two teams trying as hard as they can to win a game of cricket," Vaughan said.
"I don't think we stepped over the line. Maybe we said a few things too much in the first innings, it's just good gamesmanship. I don't think we've said anything untoward. We're trying to play tough cricket.
"The two games against India have been proper Test match cricket. They've been hard, the batsmen have found it difficult."