Villas-Boas also gave a scathing assessment of referee Howard Webb, whom he felt made some "strange decisions" during the game.
Chelsea took a first-half lead through a Jonny Evans own goal, and then raced 3-0 up inside the first five minutes of the second half through a blistering Juan Mata strike and a David Luiz header which took a wicked deflection of Rio Ferdinand.
United then hit back after Webb awarded United two debatable penalties, which were confidently dispatched by Wayne Rooney on both occasions, before substitute Javier Hernandez nodded home an unlikely equaliser late on.
Webb also turned down a strong penalty shout from United in the first half when Gary Cahill seemed to trip Danny Welbeck when through on goal, and Villas-Boas was left wondering whether that had played on Webb's mind in the second period.
"Of course, it's not easy to take," he said. "It's a massive recovery for United. We had it in our hands and let it slip.
"There were some strange decisions today [Sunday] though. These things just keep happening. The first one is a penalty and I agree with it. The second is very unlucky.
"I'm not sure if Howard is trying to compensate for something."