I just noticed that CraftTweaker2-1.12-4.1.9.jar contains these files:

[...]
      876  06-24-2018 21:56   META-INF/crafttweaker_at.cfg
    76958  06-24-2018 21:56   META-INF/fml_cache_annotation.json
    16447  06-24-2018 21:56   META-INF/fml_cache_class_versions.json
[...]
      876  06-24-2018 21:56   META-INF/crafttweaker_at.cfg
     5007  06-24-2018 21:56   META-INF/fml_cache_annotation.json
      865  06-24-2018 21:56   META-INF/fml_cache_class_versions.json
[...]

Those crafttweaker_at.cfg files are the same (I diffed them) the others already differ in filesize. Obviously, this is an error, the jar shouldn't contain two versions of the same file.

This is because there are 2 minecraft mod included, and forge generates those, and then we merge the jars, this isn't a huge issue as it doesn't actually cause any issues (to my knowledge), and will be fixed in 1.13 when the JEI support is moved out.