Trott, then batting on 43 in England's second innings total of 123 for three, tried to cut a short delivery from pacer Ishant Sharma which was taken behind the stumps by Mahendra Singh Dhoni who threw it high up in the air in delight only to see his claim rejected by Dharmasena.
Following that, Kohli ran up to the batsman and exchanged a few words after which square leg umpire Rod Tucker summoned Dhoni.
It was not clear from the TV replays whether Trott had edged the ball or not.
Later, off-spinner Ravichandran Ashwin, too, got engaged in a verbal exchange with Trott when the one-down batsman backed up too early during the bowlers' follow-through.
Ashwin stopped before delivering the ball once and warned Trott not to leave the crease or else he would run him out.
Earlier, Trott had, in a clear sign of un-sportsmanship, struck a four off left-arm spinner Ravindra Jadeja when the ball slipped out of his hand and bounced thrice before rolling wide of the wicket.
"It was nothing really. Just about the shot that he got away with the rolling ball. Just seem to us it was a little innocuous. When you talk about gamesmanship you should hold by yourself to take the same from the opponents," Ashwin said of the incident.
Trott remained unbeaten on 66 at stumps as England reached 161 for three in their second innings, an overall lead of 165 with just a day left in the Test at VCA stadium in Jamtha.
Earlier, Cook had stood his ground when he was declared out caught behind for 13 by Dharmasena and left the field reluctantly after his first twin-failure in this four-game series.
He was out for one in the first innings here.
Ashwin optimistic of Indian victory tomorrow
India off-spinner Ravichandran Ashwin is confident that the home team will be able to dismiss the remaining seven England batsmen at a fast clip thereby forcing a series levelling victory.
"Strange things have happened. We are not trying to be too optimistic, but we have done it before in India and we can take six or seven wickets in a session. It's just about trying to get a couple of wickets tomorrow morning," Ashwin stated at the post-match conference today.
Ashwin insisted that they have bowled well today.
"We have bowled well today. We are pushing for a win nothing got out of hand and we just have to stick to it, try to see if we can squeeze in a couple of wickets early morning," he added.
Questioned about India's lack of urgency to get quick runs in the morning when he was at the crease with tail-enders Pragyan Ojha and Ishant Sharma before India declared at 326 for nine, Ashwin defended the strategy saying the aim was to get as close to the England total as possible.
"We had to just wipe out the lead, eat as much into the lead as possible so that whatever they score after that it becomes an even game," said Ashwin, who tried to shield the other two batsmen by farming the strike as much as possible in the one hour that India batted before the declaration.
"(Strategy) was the same as the last game. Looking for the last two balls for the fielders to come in, but they had a different strategy. They didn't bring the fielders up. After two overs we decided to take the singles," he said.
He also said that the tail-enders cannot be expected to hit a bowler like James Anderson for a six on the slow-natured track.
"You don't have the best of ability at 9, 10, 11. You can't expect someone to smack Anderson over the top for a six on this pitch. All this game the average has been 70 and 80 runs a session."
"Basically, we were looking to take the singles. We were just looking to eat into the lead. What best we could muster we did muster. Putting it into a larger scenario, we needed to even the game. We just about did it," he maintained.
Ashwin said he cannot say that he was happy with his bowling in the series in which in which he has given away over 50 runs for each of his 13 wickets, though he had bowled well in patches.
"I cannot say that I am happy with the performance because the team hasn't won at the end of the day. It's not that I have picked up wickets and won that I am satisfied. There is always scope for improvement. There have been patches in this series that I have bowled really well. One of my best spells didn't get rewarded. That happens in Test cricket," he said.
Asked what had gone wrong with his bowling, he shot back, "Didn't I just say that I bowled a few good spells and didn't get rewarded? I think that answers your question."
Questioned what was told by him to Trott for the batsman backing up too far, he said,"(I said) I can run him out if he can hit the ball. He said you might as well run me out," the Indian off-spinner said.
"(It was) just about the shot that he got away with the rolling ball. Just seemed to us it was a little innocuous. When you talk about gamesmanship, you should hold by yourself to take the same from the opponents," he said.
Asked about the team's strategy in using its four spinners, Ashwin said that left-arm spinner have been brought on when the right-handers were at the crease generally.
"We are playing four spinners, just a guess that I am taking as much as you are taking, it's left-arm spinners to the right-hand batsmen trying to take the ball away. Especially when you have got four spinners, you are looking to rotate," he said.