Ecuador defender Piero Hincapie, a late substitute in the 2-1 victory at the Emirates, was carried off the pitch after hurting himself in the post-match session.
Arsenal boss Arteta told his pre-match press conference on Monday that Spain midfielder Zubimendi also suffered an injury in the warm-down.
"We had a training session planned after the game for the players that didn't have enough minutes to get everybody the recovery day on Sunday, and to get everybody in the right rhythm, and in two very unfortunate actions, we lost two players, and yeah, not great," he said.
"We need to assess them. Today they have further scans to see where they are, and they will have a timeframe for how long they'll be out."
The Spaniard added: "What can you do? If I knew I had a crystal ball, I'd say, 'Guys, go in the jacuzzi, everybody, and see you tomorrow.'"
Arteta confirmed both players would miss the home game against French Ligue 1 team Lille on Tuesday, adding: "Piero's one looks a little bit more serious, I think, but we have to wait and see."
Last season's Champions League finalists beat Napoli in their opening match in the competition last month.
Arsenal are second in the Premier League, three points behind Manchester City.