As the most simple example, git add both adds a new file to the index and adds changes to an existing file to the index. They are both fundamentally the same operation, but your intentions are different.
Checkout, likewise, both changes HEAD's symbolic reference and changes the working copy to match the index or a commit. This makes it both a means of full tree changes and local reversion.
And then there's rebase...
I don't think these are huge issues, but I do think they're barriers and a source of common early issues with git for new users.