The pair were hurt during a small-sided game at the Emirates Stadium on Saturday, with Mikel Arteta confirming that further scans are needed to determine the extent of their injuries and how long they will be sidelined.
Hincapie, who came off the bench in the closing stages of Arsenal's 2-1 Premier League win, was carried off the pitch after the session. Zubimendi, an unused substitute against Leeds, also picked up an ankle problem.
Arteta admitted the injuries were a setback, particularly with the Gunners facing a demanding fixture schedule.
"We had a training session planned after the game for everyone that didn't get enough minutes, and in two unfortunate actions we lost two players," the Arsenal manager said ahead of the Lille clash.
"Not great. We need to assess them today, they will have further scans to see how they are and then we will have the timeframe how long they are going to be out for."
The Spaniard confirmed both players would miss Tuesday's match and indicated that Zubimendi's injury could be the more serious of the two.
The absences also reduce Arteta's options for managing the workload of his squad, with Hincapie providing defensive cover and Zubimendi offering another option in midfield.
Despite the setback, Arteta defended the decision to hold the session, explaining that players who had not featured regularly needed additional work to maintain their fitness and match sharpness.
The training was designed to allow the entire squad to follow a similar recovery schedule, with those who had played fewer minutes participating in small-sided games before Sunday's recovery day.
Arteta said he had discussed the incident with his staff but insisted there was little reason to change the approach based on two unfortunate injuries.
"The temptation is now (to say) 'Oh we don't want to take that risk and now we do something else.' But we were going to do that the next day anyway and when you play those kind of small-sided games, there is contact and these things can happen," he explained.
He added that similar sessions had been held regularly without such incidents occurring during his time at the club.
"Never train and they don't get injured. The consequence of that is when you ask them to play they have no rhythm and no impact in the game," Arteta said.
"It's happened now and hopefully it doesn't happen again, but what can you do? If I had a crystal ball I would just say 'guys, get in the jacuzzi and I will see you tomorrow'."
There was more encouraging news regarding William Saliba, who has returned to light training. However, Arteta warned that the centre-back remains weeks away from a return to competitive action.
Kai Havertz and Ezri Konsa, meanwhile, were able to train after recovering from injuries sustained during the international break and featured against Leeds.
Arsenal must now prepare for Lille without two further options, while awaiting a clearer picture of the damage sustained by Hincapie and Zubimendi.
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