Put in to bat on a green-top wicket by England skipper Alastair Cook, India collapsed to 140 for six by tea, only to be rescued by Ajinkya Rahane's 103 that helped the visitors end the day on 290 for nine.
"It is a little bit frustrating, especially with their tail doing well," said Stoke, who claimed one for 40 in the first innings.
"But credit must go to Ajinkya Rahane for the way he batted. It was a really good knock from him and we can take positives from the fact that we restricted them to 140-odd runs for seven wickets before he played that knock," he said.
India were struggling at 145 for seven before a 90-run partnership for the eighth wicket between Rahane and Bhuvneshwar Kumar (36) saw them end the day on a high.
"Kumar seemed to hang around quite well. He played and missed on a number of occasions but his nicks went into the gaps. We had a long, tough day in the field," said Stokes.
When asked if England were guilty of bowling poorly, he replied, "No, we were happy with our lengths but our lines could have been a bit tighter in the morning, more towards the stumps. The movement was a bit excessive compared to Trent Bridge and we corrected it. They had played a lot more and missed in second session and we got quite a few wickets then.
"But bowling short in the last session wasn't my plan. I wasn't privy to the chat between Jimmy and Cook.
"Shami was looking alright, so the plan was to get him off the strike and target Ishant Sharma's wicket," he added.
James Anderson finished as England's best bowler on the day taking four for 55, especially at the backdrop of physical abuse charge levelled against him by India, and Stokes was all praise for the pace spearhead.
"Full credit to him, the way he has bowled today. It is good to concentrate on cricket and try to be professional. He showed that today and it was good to watch him bowl like that.
He is very consistent and knows his game inside out. He plays the game hard and sets up batsmen. Hopefully, I can play at his level one day," Stokes signed off.