as two goals from Braga captain Alan stunned Old Trafford into silence.
For the eighth time in 12 matches this season, United were forced to come from behind after conceding the opening goal.
While Ferguson was full of admiration for the Hernandez-inspired fightback, it was revealing that, without any prompting, he launched into an analysis of his team's problems at the back during the post-match press conference.
Even more intriguing was Ferguson's revelation that he doesn't have a cure for the careless way United are surrendering so many goals.
There was no disputing the quality of Alan's strikes in the 2nd and 20th minutes: but the failure of Alexander Buttner to close down the playmaker for both goals, combined with the ease with which Hugo Viana and Eder were allowed to provide the assists, has given Ferguson serious cause for concern.
"I can't understand our defending, I can't get to bottom of it at all," Ferguson said.
"If you analyse all the goals we are losing they are all different types. Today it was a cross, then a cutback into the box with players free.
"I can't put my finger on it, but we aren't getting good starts to games that's for sure. It's making it difficult for us.
"It's interesting that it's the home games when we are conceding early goals, but we'll sort it out eventually, I'm sure of that."
Fortunately for Ferguson, while Braga proved adept at exploiting United's flaws at the back, Jose Peseiro's side had plenty of holes in their defence as well.
Mexican striker Hernandez started the revival with a 25th minute header from Shinji Kagawa's cross, then Jonny Evans equalised with a scuffed 62nd minute shot.
That set the stage for Hernandez to head the winner from Tom Cleverley's cross with 15 minutes remaining.
"Our forward play is getting us out of holes all the time," Ferguson said.
"We produced some fantastic football and in the second half kept a really good momentum and speed to our game.
"We got a result people wouldn't have expected when we were 2-0 down. Credit to the players, they don't stop."
Ferguson reserved special praise for Hernandez, who endured something of a sophomore slump last term after a blistering debut campaign with United.
Hernandez faces a tough battle to hold down a regular place as he competes with Rooney, van Persie and Danny Welbeck, but Ferguson admits it is a selection headache he is happy to have.
"The boy is improving all the time. He's a fantastic trainer and practises all the time," Ferguson said.
"He's given me a problem and I think that's good. His goal ratio for us is fantastic.
"For his second goal, his movement was terrific. He bent his run behind the defenders."
It was the first time United had recovered from two goals down to win in a European tie since they beat Juventus in the semi-final of their triumphant 1999 Champions League campaign.
But Ferguson, whose side are firmly on course for the last 16 after winning their first three Champions League group fixtures, didn't take it as a good omen.
Instead he insisted that the same kind of careless defending would be punished by more formidable opponents later in the competition.
"I'd rather do without it, it must be said," Ferguson added. "It's hard enough being 2-0 down in a normal game but in a European tie it's very difficult."