Gundogan has participated in all 42 Barcelona matches this season.
Nagelsmann said: "Illy plays 90 minutes each game for Barcelona. He's not that fresh, he has a lot of games under his belt, and he can blame that."
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The coach's comments come after Ralph-Uwe Schaffert, vice-president of the DFB, stated: "Ilkay Gndogan, for example, strangely plays in an outstanding way for the club and then plays in such a way for the national team that one can come to think: Has he sent his twin brother, with less talent?
"I don't understand it."