The author of software can release his work under any number of licenses, or none at all. An author can release the same code under MIT, Apache, GPL, MPL, or commercial license at the same time.
If the code is tagged as being MIT in GitHub and includes an MIT license file, can an author reasonably argue that an end-user is receiving the code under a different license?
Maybe. MIT license permits additional license restrictions on top of license. For example, MIT code can be copied into a proprietary system with a different license, which will forbid copying code out.