Sure. She could steal important ninja tools that were meant for the main characters in the fanfiction, thus derailing their mission. For example, if Naruto and his team were supposed to retrieve a special kunai for a crucial battle, Anko could take it first.
In Naruto fanfiction, Anko could also be portrayed as a double agent. She could pretend to be on the side of the good guys but actually be working for the villains. This would mess up the trust dynamics in the story. For instance, she could lead Naruto and his friends into a trap while they believe she is guiding them to safety.
Anko might insert herself into a romantic subplot in the fanfiction. Let's say the fanfiction was setting up a relationship between Naruto and Hinata. Anko could start flirting with Naruto and causing jealousy and confusion, completely changing the romantic direction of the story.