The specific artifact that I was using had duplicate classes, using fabric loom it remaps one of the classes and leaves the other in intermediary.

The specific maven artifact in question is: appeng:appliedenergistics2-fabric:10.0.0-alpha.7:api

Example of one of the non remapped duplicate classes

EDIT: After looking through the various artifacts, this seems to only affect the api. The duplicated classes are of compiled class files and uncompiled java files

Yeah that has always been like that. The api jar was always simultaneously a source jar and that is intentional.
Loom has a lot of remapping issues overall :| The only thing you can kinda do is detach the source and rely on the decompiled IntelliJ source.