Klaas-Jan Huntelaar gave the Bundesliga side the lead in the 76th minute and Ibrahim Afellay secured the victory 10 minutes later to condemn Arsenal to their first Champions League group-stage defeat at home since 2003.
The Gunners looked completely devoid of ideas going forward and Arsenal captain Vermaelen was frustrated not to have been able to bounce back from Saturday’s defeat at Norwich.
“I’m really disappointed,” Vermaelen told Sky Sports. “We lost on Saturday and we wanted to do better today.
“I think it was a little bit of the same story as Saturday: we couldn’t create enough chances to score goals. We conceded one goal and after they countered us and the result’s 2-0.
“It’s difficult to explain. We gave 100 per cent but it’s a little bit difficult at the moment. We don’t create enough chances to score goals.
“These moments are difficult but you still have to work hard every day and at the end it will be OK.
“Teams come here with strong organisation. We know we have a good technical ability but they come with a defensive shape all the time and sometimes it’s difficult to get through that.”
The result drops Arsenal into second place in Group B, a point behind Schalke – and Huntelaar admitted his delight at seeing his side leapfrog the Gunners.
“We’re very pleased,” he said. “I think we played well. We had our chances and we scored two goals so from our side it was a good game.
“It was really good for us, now we have seven points. For us it’s looking really good now but we have to go on; we have three matches left and we have to win those too.”
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