Naruto's ability to create a large number of shadow clones could be a major factor. In the Star Wars universe, the Jedi might see this as a form of over - powering or unethical power use. They could misunderstand his intentions and think he's trying to overpower them, leading to the feeling of betrayal. For example, if Naruto uses clones to scout a Jedi - held area, they might think he's spying on them for an enemy.