Legacy application files (for example, EXEs) are not assessed - they are given a neutral (grey) RAG status. You can repackage them selectively using Convert > Repackage at the top of the screen. Refer to The Repackaging Process.
You can also initiate the Virtualization of any of the MSIs or EXEs via Convert > Virtualize at the top of the screen. Refer to The Virtualization Process.