Playmaker Henrikh Mkhitaryan is also a doubt for the trip to Spain.
The Armenia international returned from the sidelines against his former side, scored the leveller but was forced off in the second half after picking a knock to his recuperating knee.
“Mkhitaryan I took off because he had a little knock on his knee again, the same thing, just looking at him in the dressing room,” Wenger said.
“Ospina has a rib problem and Alex Iwobi has a hamstring problem.
"We’ll see how everyone recovers because Thursday will come around very quickly.”
Last week at the Emirates, a wasteful Arsenal side were held 1-1 by 10-man Atletico - who also had manager Diego Simeone sent off.
And when asked if any of the injured trio will miss the decisive second leg at the Wanda Metropolitano, Wenger said: “Definitely at the moment no.
“But we will have to monitor them in the next 48 hours. We will know more on Tuesday.”