Perhaps a powerful ninja who doesn't like the idea of an outsider like Miku in their world. This ninja might see Miku as a threat to the traditional ninja way of life and decides to get rid of her. They could use their knowledge of the ninja arts and the terrain to set up traps and attacks against Miku and her new - found friends in the Naruto world.
It could be someone from Miku's world who follows her into the Naruto universe and has evil intentions. Maybe a jealous rival who wants to stop Miku from becoming popular in the new world.
There could be a dark force that is awakened by Miku's arrival in the Naruto universe. This dark force could be something that has been sleeping for a long time and Miku's unique energy stirs it up. It then becomes the main antagonist, trying to destroy both Miku and the Naruto world. It might have the ability to corrupt the minds of the ninja and turn them against Miku.