Arsenal are waiting anxiously on the results of a scan to hear how long the hamstring injury picked up by Cesc Fábregas during the 2-0 defeat by Braga will keep him out of the side.

Following the match Arsène Wenger said his captain might be out for about three weeks and he will definitely miss the trip to Aston Villa on Saturday. The club may target the game against Manchester United on 13 December for his return.

Fábregas has been plagued by hamstring problems since the start of last season and recently missed a month of football. Wenger warned that it had become a mental issue for the Spaniard, and the subsequent injury was to Fábregas's right hamstring rather than a recurrence of the problem he had been suffering in his left leg, meaning he is now struggling to overcome damage to both.

Glenn Hoddle, the former England head coach and Tottenham Hotspur midfielder, said this may have been due to Fábregas subconsciously shielding the original injury. Speaking on Sky Sports' Champions League coverage, Hoddle said: "Once you have a hamstring [problem] on the left-hand side you can also do your right one. You compensate. You think you're over the injury and sometimes you're not and you just compensate and can end up getting [a further] injury, whether it be another hamstring or an achilles [problem] on the other side of the body. That's what I've experienced over the years. He's going to be in trouble because the difference with hamstrings is that you've got to clear it up and this has been going on for too long. How do you clear it up? Time."

While Emmanuel Eboué also suffered a medial ligament injury that will keep him out for weeks, Fábregas's absence in central midfield is compounded by concerns regarding the team's frailties. The defeats by Braga and Spurs in Arsenal's previous outing were due to goals being conceded through the middle of the defence.

Against the Portuguese team Arsenal required only a draw to qualify for the knockout stage of the Champions League but the sudden collapse occurred when Matheus was allowed to run through the midfield and defence to score twice in the closing moments.

While Wenger's players queued up to apologise and state that it was unthinkable they would now fail to progress in the Champions League, Johan Djourou did accept that concerns regarding the side's robustness has become an issue. "That's normal but I think we are big enough to stand up for ourselves and be ready for the next game," he said. "Of course if Arsenal do not go to the knockout stages it's a disaster and I think that shouldn't happen. I don't even think that we're not going to qualify. We have to think positively. Obviously we're very disappointed but the season is still long and we can still qualify even if we would have preferred to be qualified [now]."

Despite the Spurs defeat Arsenal are two points behind the league leaders, Chelsea, and know victory over Partizan Belgrade at the Emirates in a fortnight secures qualification. With the club also still in the Carling Cup – they host Wigan Athletic on Tuesday in the quarter-finals – Djourou is confident they can finally win something this season. "Of course we can, we want to win a trophy. That's the main focus of the team and we've got the quality to do it. Luckily we're not too far from the top [of the league]. Hopefully we can definitely win a trophy this season."

Denilson, whose performance along with his fellow holding midfielder Jack Wilshere was disappointing, apologised. He said: "It's very disappointing and I feel very bad and very sad about this. For the fans I should say sorry and for the last match [against Spurs] as well. We have to win trophies this season because this is very important for us."

The Brazilian is confident that Arsenal will not slip up against Partizan. "I believe we will go through and qualify – you always have to believe that. We have one more game against Partizan at home and we have to be strong in this game."

Wilshere wrote on his Twitter page: "Would like to apologise to all the supporters, especially the ones that travelled, for the result last night. Still can't get my head around how we can loose [sic] this game after dominating for so long."