I've got two situations when refactoring goes mad:
1. Create a class and a object with the same name under a file, add a method to both of them (different ones to each one). Try to copy and paste the file to another IntelliJ project. The class is copied twice and the object is not. Or the other way around. I have a feeling it also happens when moving it within the project
2. Moving classes around do not update correctly the imports. So if you move a class from one package to another, where another class used to import the original one, now it gets crazy and imports it twice, even though the first import does not exist.