Spurs lost Steven Bergwijn and Lucas Moura to injury and with Son Heung-min already battling a calf issue, Nuno is looking short of options for Sunday's Premier League clash with Chelsea.
That is in addition to having Cristian Romero, Giovani Lo Celso and Davinson Sanchez out of action for the last two games as they quarantine in Croatia after they defied Premier League rules to travel to South America for international duty a fortnight ago.
On a tough evening in France in arguably their toughest assignment of their Group G stage, the Portuguese saw his side go ahead early on through a Loic Bade own goal before the French team hit back either side of half-time through Flavian Tait and Gaetan Laborde.
Pierre-Emile Hojbjerg's leveller earned Spurs a point, but Nuno is frustrated at the situation.
"It's been terrible. I must be honest. Let's not hide behind anything," he said. "After the Watford game, everything that has happened has not been very good for us.
"But this is football. And we know it's a moment we have to overcome.
"Today, we tried to show the players solutions, thinking about the game on Sunday. But it's about overcoming obstacles. That will make us stronger for the future, for sure."
Asked whether Bergwijn or Moura would be fit for Sunday's game, he said: "Painful, really bad. I cannot tell you. They are being taken care of by the medical department. But it's been tough."
Considering their selection issues and how the game went, taking a point home from Roazhon Park is not the worst result for Spurs.
Nuno said he could not be too judgmental of his side.
"(It) was not perfect. I think we started very well in possession, finding good lines," he added. "We scored, then we lost a little bit of control. Rennes is a good team, they caused some problems for us.
"It is hard to judge all the game with all the circumstances that happened during the game.
"But I think we finished well, we showed a lot of character and belief to change the result after we conceded.
"In the end I think we were in control. A hard team to play, a hard pitch to play, but the attitude was good... a lot of players out of position so it is hard to analyse and be fair."