United came from 4-2 down in extra-time to win the Europa League quarterfinal second-leg 5-4. United reached the semis 7-6 on aggregate.
Fonseca said afterwards: "It's hard to explain, a mix of emotions because the players did great things, conceding two goals and having the ability to go to 4-2 with a player down, it was magnificent, I'm very happy with my players but I'm sorry.
"We thought the result was a given but we had to stay focused, we lacked mental energy, we lacked emotional balance, I'm sad because I think we deserved more, we proved our qualities and we have to learn from these moments."
"We must play to last minute"
Indeed, Fonseca admits Lyon failed to play to "the last minute".
He also stated: "We must always continue, until the last minute. We have to understand what we did here.
"We did magnificent things, it's not easy to play against Manchester, to turn the situation around but we just have to learn from this scenario. We have proven that we are ready to have an end to the season that lives up to our ambitions."