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.
