The teams will meet again at Old Trafford on Wednesday for the fourth Test with India, 2-1 down in the five-match series, forced to make changes.
Fast bowler Akash Deep is out with a groin problem, joining allrounder Nitesh Reddy and fellow pacer Arshdeep Singh on the sidelines. Right-arm quick Anshul Kamboj is likely to make his debut having been drafted into the squad on Monday.
"Anshul is very close to making his debut. We're going to see tomorrow between him and Prasidh (Krishna)," said Gill.
The flashpoint that led to ill-feeling at Lord's occurred on the third evening, when England's openers had to bat out the final seven minutes but India only got through one over.
Zak Crawley repeatedly pulled out of his stance to Jasprit Bumrah, then called for the physio after being rapped on the finger, leading an irate Gill to shout an obscenity towards the England batter.
But while Gill begrudgingly accepted the time-wasting tactics when the players were on the pitch, what he was especially unhappy about was Crawley and Ben Duckett being late to the crease in the first place.
"A lot of people have been talking about it, so let me just clear the air once and for all," Gill said.
"The English batsmen on that day had seven minutes of play left, they were 90 seconds late to come to the crease. Not 10, not 20 - 90 seconds late.
"Yes, most of the teams use this. Even if we were in this position, we would have liked to play less overs, but there's a manner to do it. If you get hit on your body, the physios are allowed to come on and that is something that is fair.
"But to be able to come 90 seconds late to the crease is not something that comes in the spirit of the game."
Gill added there were other issues at play.
"I wouldn't say it's something I'm very proud of but there was a lead-up and build-up to that - it didn't just come out of nowhere.
"We had no intention of doing that whatsoever but you're playing a game, you're playing to win and there are a lot of emotions.
"When you see there are things happening that should not happen, sometimes emotions come out of nowhere."
England captain Ben Stokes, speaking before Gill, says his side will not seek to deliberately antagonise India for the rest of the series, but insisted they will not shrink away either.
The England skipper again criticised over-rate assessments after his team were docked two World Test Championship points after the Lord's Test.
"You can't have the same rules in Asia where spin is bowling 70 per cent of the overs to have the same laws in New Zealand, Australia, England, where it's going to be 70, 80 per cent of seam bowled," said Stokes. "Common sense would think you should look at changing how the over-rates are timed in different continents."
England have replaced injured spinner Shoaib Bashir with Liam Dawson.
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