The impressive Spaniards also inflicted United's first back-to-back European losses at Old Trafford since 1996.
"There has been that slackness all season," Ferguson said. "We have had a bad year in Europe."
United at home in Europe
Man Utd 3-3 Basel
Man Utd 2-0 Otelul Galati
Man Utd 2-2 Benfica
Man Utd 1-2 Ajax
Man Utd 2-3 Athletic Bilbao
"We conceded three against Basel, two against Benfica, another three against Bilbao and two to Ajax. That tells its own story.
"Maybe it is just one of those years where we are having to restock and assess how we should approach games at home."
Goals from Fernando Llorente, Oscar de Marcos and Iker Muniain condemned United to successive home defeats,
following last month's 2-1 reverse by Ajax,
for the first time since Fenerbahce and Juventus each claimed 1-0 Champions League wins 16 years ago.
Ferguson admitted his side were outplayed by Bilbao on Thursday but insists they can overturn the first-leg deficit.
Wayne Rooney's early goal gave United the advantage before Marcelo Bielsa's fifth-placed La Liga team hit back to take a deserved 3-1 lead.
However, Rooney scored an injury-time penalty to give United a glimmer of hope ahead of next Thursday's second leg in Bilbao.
Manchester United boss Sir Alex Ferguson admits Athletic Bilbao were better
"They were the better team. It's an uphill fight for us," said Ferguson.
"The question is, can we win the match over there? I think we can."
But the Scot complained De Marcos's goal should have been ruled out for offside and felt German referee Florian Meyer made an error awarding a free-kick against Patrice Evra for kicking the ball without his boot on in the run-up to the third.
"The referee said to the players that you can't play without a boot," added Ferguson.
"The real rule is you can but when the play is stopped you have to go off the field.
"It seems a bit bizarre as he only passed it about three feet. It was a bit unfortunate."
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