Try this:
1. Grab Dex2Jar from here hxxps://github.com/pxb1988/dex2jar/releases/tag/2.1-nightly-28 and unpack it to a folder
2. Take the sample I attached, some old APK I had lying around with these duplicates
3. Extract the .dex file from within: "unzip *.apk classes.dex"
4. C:\...\...\d2j-dex2jar.bat classes.dex
5. Look at the output jar, it has the duplicates: "jar tf classes-dex2jar.jar | findstr com/a/a/ac/[aA]\.class" - 2 separate files exist for that package, for instance (more exist)
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