The mp4 type is a container type and can hold different things inside it. The MIME checking is for verifying that what is advertised to be in the file matches what is in there (as far as can be done).
You might find better checking using the plugin Lord of the Files, and if you still have trouble, ask at that support forum because the author will help you debug it and update the checking function if you found a case that isn’t handled.
Thanks for the suggestion @joyously, that plugin has resolved the false detection problem of that file for me. Thank you!!!
Shame that we have to rely on plugins to fix WordPress’ shortcomings.