In the Champions League round-of-16 fixture, an injury-hit Spurs slumped to a 1-0 defeat at home to RB Leipzig. Meanwhile, Serie A side Atlanta thrashed Valencia 4-1 at home.
Spurs could be without the talismanic duo of Harry Kane and Son Heung-min for the rest of the season through injury and looked toothless against the Bundesliga contenders.
"We are in a very difficult situation," said Mourinho. "What worries me is this is going to be the situation until the end of the season."
Tottenham captain Hugo Lloris kept his side in the tie with a string of important saves, but he could not prevent Timo Werner from the penalty spot as the German international's 26th goal of the season gave Leipzig a lead to defend on home soil on March 10.
"Over the 90 minutes we deserved the win and could have won by more," said Leipzig boss Julian Nagelsmann.
"It's only the first game today. You have to perform at the same level in both games."
Tottenham upset the odds to progress past Manchester City and Ajax to reach last season's final. But it was Leipzig who looked the seasoned Champions League team in their first-ever knockout tie in the competition.
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Meanwhile at San Siro, Atalanta thrashed visitors Valencia in a 4-1 victory. Atalanta manager Gian Piero Gasperini was not entirely satisfied with the victory and seemed hungry for more.
"We need to be more precise when we go to the Mestalla," the Atalanta coach told Sky Sport Italia.
"If we want to get into the quarter-finals, we have to play like this at the Mestalla too, prove we deserve to be there with a show of strength, and win there too."
Spurs will look forward to making a comeback at the Red Bull Arena during the second leg fixture against RB Leipzig and Atalanta will visit Mestalla to play against Valencia.