Defender Diego Llorente limped off in pain, while forward Paulo Dybala had trouble with his ankle after a heavy tackle.
"We ended the match with nine men and still hit the upright, which would have been 3-2. It is very, very difficult for me to be critical of this squad. They play within their limits," Mourinho told DAZN.
The latest injuries add to the manager's concerns as Rick Karsdorp, Chris Smalling and Georginio Wijnaldum are all sidelined at a time when Roma face important matches.
"I think every coach even in the richest clubs will have a problem when players are missing. For some teams it is a small problem, for us it is a huge problem," Mourinho said.
"Smalling is Smalling, Diego was adapting very well and now he too is out. Obviously, it will be very tough for us."
On Saturday, Roma host fourth-placed AC Milan, who are level on 56 points with Mourinho's side. Roma must also play Monza and Inter at the beginning of May before facing Bayer Leverkusen in the Europa League semi-final first leg on May 11th.
“We have to think game after game, with the risk of not making it to the Champions League, but there is also the chance of winning the Europa League," said Mourinho.
"This is a united team, in difficult moments we are always together and I think the fans are also proud of this team," Mourinho added, saying he recently rested key players on the bench to save them from injury.
"Injuries are due to the accumulation of matches. What we tried to do today was protect those players who the medical staff showed had more fatigue after Thursday’s match, specifically Leonardo (Spinazzola) and Nemanja (Matic)."
Roma won 4-1 against Feyenoord on Thursday in their Europa League quarter-final, second leg to progress 4-2 on aggregate.
