The Gunners are having an injury crisis in this position, with only Shkodran Mustafi and Gabriel Magalhaes fit to play.
The issue is that Sokratis Papastathopoulos and Saliba are at the club, but neither is in the team's 25 man Europa League squad.
"I feel really bad for William Saliba," Arteta told reporters.
"Because we had so many central defenders, we decided to leave him out of the squad which was really hurtful for me to do.
"I was hoping that Pablo would be back in two weeks but he had a setback and then we don't have Pablo and we don't have William when he's fit and available to play.
"But when you make those decisions, you can't always think about every possible outcome."
Asked to say more about Saliba, Arteta added: "Yes, he's in a much better place.
"He's feeling a lot more confident around the place, his language is improving and he's starting to understand much better what we're doing physically.
"He's played a few games with the under-23s which he needed because he didn't play any football in the last seven or eight months. Things are progressively getting better and better."