The 28-year-old South Korean pulled up with what looked to be a hamstring issue after chasing a pass and was replaced by Erik Lamela, who netted the opener for Spurs after 33 minutes.
Martin Odegaard and Alexandre Lacazette hit back for Arsenal to seal the win.
“I don’t know how long it is. It’s muscular. Muscular is usually not easy,” Mourinho told reporters, adding that the problem was caused by playing too much.
“He’s normally a guy who recovers quickly. It’s (because of) an accumulation of matches. In the Europa League, I gave him 30 minutes rest in the last match, but it’s still 60 minutes,” Mourinho added.
“And when you’re in so many competitions, some players they have more minutes than others, which is normal, something that can happen.”
Defeat left Mourinho’s side in seventh place with 45 points, six behind Chelsea in fourth — the final Champions League qualification spot.
Tottenham travel to Dinamo Zagreb in the Europa League last-16 second leg on Thursday before visiting Aston Villa in the league on Sunday. — Reuters