With two minutes remaining, M’Bia (left) appeared to pull down Wayne Rooney (right) after a poor first touch by the defender put the England striker through.
Referee Felix Brych decided it was not a foul but Ferguson remained convinced that he should have been sent off for a last-man foul.
"I think it was very lucky, the referee's in a good position and I don't know why he didn't give us a free-kick and then the decision is straightforward - it's a red card," Ferguson told ITV afterwards.
"(The performance) was disappointing, the pitch was lively but they made sure they weren't going to lose a goal. We got in good positions but we didn't have enough.
"Nil-nil can be a dangerous scoreline if you lose a goal at home but it's about winning the game, if we win the game we're through. We're confident, I think we'll be much better."
Marseille coach Didier Deschamps was pleased with the result, and said: "For the first game it is very important you don't concede a goal. We have done it, it was a tough game because Manchester are a big team.
"We had a very good spell in the second half for 20-25 minutes but we couldn't find a goal.
"I am very happy for my players, they have done their best. It is important for the return to not concede a goal again and, if we get the opportunity, to score.
"Manchester are always favourites, it's not a bad result for us but it is a good result for Manchester."