There are several instances where injured Naruto used shadow clones:
While fighting with Kabuto, Kabuto severed the muscle and tendon of Naruto. Later, when Naruto used a shadow clone to make Rasengan, did the shadow clone have the same injury as Naruto?
After the final fight with Sasuke (i.e. after defeating Kaguya), were the shadow clones of Naruto missing their right arms [before being treated by First Hokage, Hashirama's cells]?
Apart from these two, even thoroughly exhausted Kakashi used shadow clones after defeating Zabuza. Were these shadow clones injured?