Android projects have different build types like "release" and "debug". It's valid to put a class with the same name into the debug and release folder. When both source folders are indexed and imported by the IDE at the same time, then the IDE complains about a duplicated class, what is a false positive. Usually, the IDE doesn't index both build type folders, but this is especially helpful for refactoring.
At the moment there is no way to suppress this error. To be clear, I'm referring to this check: https://github.com/JetBrains/intellij-community/blob/2d38669630890eff5f1a03a29ce4800bb8287858/java/java-analysis-impl/src/com/intellij/codeInsight/daemon/impl/analysis/HighlightVisitorImpl.java#L426
I as a developer should have the option to suppress or disable this error. If I did something wrong, then the compiler would complain anyways.