United suffered their second successive home defeat in the tournament as impressive Athletic came from behind to win on the night.
Wayne Rooney put United ahead, but Fernando Llorente headed an equaliser before the break. Athletic then turned the screw as Oscar De Marcos put the Basque side ahead and Iker Muniain capitalised on Rafael's defensive lapse to make it 3-1.
Rooney's injury-time penalty reduced the areas, but the Red Devils face a tough task to turn it around at San Mames next week.
"We were well beaten, I have to say they were the better team," Ferguson told Channel Five.
"I thought our defending wasn't very good tonight [Thursday] and that kept us on the back foot all the time. Our attacking play was very good at times and it was an open, entertaining match. But Bilbao were the better side.
"We can still win the game. No question. We showed we can make chances against them, but obviously we have to defend better.
"I need to really look and see how we can maybe bring Rio Ferdinand in without disrupting the league programme."
Ferguson criticised referee Florian Meyer's decision to award Athletic a free-kick in the build-up to their third, apparently because Patrice Evra passed the ball after his boot had come off.
"The third goal, I don't know how you describe it. The referee's stopped play...the issue that Patrice didn't have a boot on, they say you're not allowed to do that. But he only passed it about two feet."