The Marina Machans rallied from a goal behind in their clash in the final eight where Anirudh Thapa assisted one for Mailson Alves and scored the winner himself.
The coach of the former champions, John Gregory, was livid after seeing NorthEast players targetting Thapa with numerous rough challenges.
"We have tried to look after Thapa as well as we can. He is our player, contracted to us for a long time. I want to try and look after him. In the last couple of years, he has been involved in the senior team, U-23 and with us. We are just trying to manage him in the right way. He is a better player now than he was a year ago. He has got to keep improving," said the 64-year-old.
Thapa was brought down to the ground at least a couple of times by the likes of Girik Khosla and Jose Leudo and Gregory couldn't help mentioning that the challenges went unpunished.
"I don't like to see players getting cards. But they (NorthEast) did seem to target Thapa. Every time he got the ball, he got fouled badly. I need him protected, you expect the officials to protect your players, I don't think they did that enough. Chris Herd made one tackle and got a yellow card immediately. I was a little bit angry," Gregory admitted.
Meanwhile, Chennaiyin tactician wants to put his side's embarassments of a poor Indian Super League (ISL) season behind them. In the inaugural edition of the Super Cup too, Chennaiyin were knocked out by Aizawl FC in the Round of 16 where they fielded a weakened outfit.
"We still have got lots of problems but we are coping with it. We got our backsides kicked [in the Super Cup] last season and we came in wanting to give it our best. We are focused on it. The players have been working hard and encouraging one another. We are embarrassed by the season we had. By being successful in two cup competitions, we give us a much better feeling. We had to fight really hard tonight. Overall, we deserved the win," he signed out.