Jarrod Bowen had given the Hammers the lead in the 73rd minute but Georginio Rutter levelled matters late in the match.
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Rutter had mistakenly handled the ball before finding the next against the Londoners and Nuno felt the goal should not have stood.
"It was a handball, wasn't it, and a high foot. No need to speak with the referee. I think it was the main factor,” Nuno told Sky Sports.
“It's clear. I saw it, everybody saw it. VAR saw it, everybody saw it. I think both situations should be checked.
“It's hard to take, man, it's really hard to take, especially after the hard work of the boys, the support of our fans that makes us feel like we were in London.
“Then comes one situation, so many people see it, it's hard to take."