Mach-O 64-bit executable x86_64 are used by OS-X, iOS, and some other operating systems derived from the MACH kernel. The only one of those that runs MATLAB these days is OS-X. However, OS-X does not use the .exe file extension, which hints you might be trying to execute the file on the wrong machine.
However, it is true that on Unix derivatives, the file extension is not the important feature for determining whether a file can be executed from the command shell by direct reference the way you show using ./file.exe . Instead what is required first is that the file have its execute permissions set as far as the user is concerned. If the execute bits are not set then you would receive a "Permission denied" message.
With the execute bits set, the operating system would look at the "magic number" to try to determine how the file should be executed. For text files, the "magic number" is "#!" as the first two characters of the file. For Mach-O 64 bit binaries that do not show up as "fat" binaries, the magic number involves in part the file starting with hex FE ED or hex CF FA. "file" indicates that those bytes are properly present in the file. If you were using OS-X and those bytes were not present then you would get an error message about trying to execute a binary file; likewise if you were using some other operating system and trying to execute mach-o files then you would get the same message. For example you would have a problem if you tried to execute such a file under Linux.
At this point we are stuck because we do not know which operating system you are running.