The Catalan outfit came behind to lead 2-1 at the interval of the last-eight affair, but Oihan Sancet levelled the scores at 2-2 before Inaki Williams and Nico Williams netted in extra-time to hand Athletic a 4-2 win.
The defeat was even more damaging for Barcelona, though, with Alejandro Balde, Andreas Christensen and Ronald Araujo picking up injury problems.
Balde was forced off in just the 23rd minute of the fixture, and according to Mundo Deportivo, he will undergo a scan on Thursday to determine the extent of the damage.
The Spain international's issue is said to be related to his thigh, and he was in tears as he left the field, hinting at a potential lengthy absence for the full-back.
Christensen, meanwhile, recovered from a muscular problem which forced him to miss out against Real Betis in La Liga last time out to feature in the middle of the defence.
However, the centre-back was withdrawn in the 70th minute due to a calf issue, and he had ice on the impacted area while sitting on the bench.
Christensen is also set to undergo a scan on Thursday to determine the problem, and it seems likely that he will at least be absent against Villarreal in the league this weekend.
Araujo was able to complete the 120 minutes, but the Uruguay international suffered a blow to his knee, and he revealed after the match that the problem has been causing him issues over the last couple of weeks.
«Well, the truth is that it bothers me. I've had it for a couple of weeks now, but I always want to be there,» he told Mundo Deportivo.
Hector Fort and Pau Cubarsi have benefitted from the team's
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