Yes. You asked Matlab to include the txt file, so it did. If you don't want to include it in the packaged app, you shouldn't add it as a required file, even if on another level the file is required.
To explain it in a different way: your program may require manual input to be valid, but that is not a requirement for your program to start without fatal errors. Incorrect input should be dealt with in the program itself, not by the compiler.
