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they sealed a clone
madara went to get his second rinnegan from obito in the other dimension
when he came back out with both eyes they were surrounded by madara and 4 of his limbo clones
Yeah, you need to go back and re-read the story. They were about to seal Madara, who replaced himself with his Limbo clone to go get his other eye, and the clone ended up getting sealed.
Madara returned from the Kamui Dimension, in front of Naruto, Sasuke, Kakashi, and Sakura, surrounded himself and Obito/Black Zetsu with his clones, as a defense
Sakura attacked him, got stabbed, and had Naruto and Sasuke save her. Madara then flew up and cast Infinite Tsukyomi.