Tonel does not generate duplicated method.
However, they can appear via git merge.
With @jecisc , we think that Tonel should have an option to check the consistency of a .tonel file that should be disabled by default in development images but enabled on the Pharo CI.
Like that, people can load corrupted tonel project during development but we can ensure that Pharo repository has no corrupted tonel files by enabling this option on the CI.